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github.com/Bioprotocols/labop

Laboratory Open Protocol (LabOP) Language
https://github.com/Bioprotocols/labop

applied black formatting

0cf6e6a184671f44c27a8edd077e8dff94cb9efa authored over 2 years ago by Daniel Bryce <[email protected]>
checkpoint

4da867fda47acc183225961270550759f6fb9fba authored over 2 years ago by Daniel Bryce <[email protected]>
clean up and fix finalnode semantics

bcd6a0b23edd754ab8328376056920752e24255e authored over 2 years ago by Daniel Bryce <[email protected]>
helper function for decision nodes

5b814ca09a1e364e40455cf01bf0bed59658456e authored over 2 years ago by Daniel Bryce <[email protected]>
Initial implementation of DecisionNode w/o else

45cc62b383e765e4e413f87e52e0cd43f2cf84e8 authored over 2 years ago by Daniel Bryce <[email protected]>
Cherry pick specialization from Friendzymes fork

ebcc32925161b872713b009a46f25c90e468e9dc authored over 2 years ago by Bryan Bartley <[email protected]>
Setup place to add conversion to opentrons. Based on Autoprotocol conversion by removing specifics.

30671e252269cc07281d127b09f65edc0a30b061 authored over 2 years ago by Daniel Bryce <[email protected]>
Update notebook examples to support markdown attribute on Execution objects

a4be2a5e0906980f39f965543bb6ba80fd211cc6 authored over 2 years ago by Bryan Bartley <[email protected]>
Remove extraneous newline from test files, resolves #150

9e7e09929c5c08b5670285757e3ae7cc8d9a4832 authored over 2 years ago by Bryan Bartley <[email protected]>
Resolve #151, save CI testfiles as artifact

6d02b0394757996cbe4dcf8c99d84ba4dadf74ef authored over 2 years ago by Bryan Bartley <[email protected]>
Skip test

464a02793bfb89a9fc0452cc9855bf23964ab46d authored over 2 years ago by Bryan Bartley <[email protected]>
Update test file

a0b4e2defe0b3789189e799f370bb53e294fbe91 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix _materials breaks when a container spec can't be resolved

202c1567b03b3d01617cab00c4f3f6493f5749ca authored over 2 years ago by Bryan Bartley <[email protected]>
cleanup pages

61d1ec0aa12a1674d6e6df9e9f727e778910a383 authored over 2 years ago by Daniel Bryce <[email protected]>
Handle container exceptions better

4ce9211aa03b9634f264a8bc3ba348db9810a1ac authored over 2 years ago by Bryan Bartley <[email protected]>
Turn on failsafe

8c27f015cda0dccf22d010268a83cef6ddbf9d35 authored over 2 years ago by Bryan Bartley <[email protected]>
Update pages.yml

6a9b8f0862c3d1ee78d6ba9b3bb685a88d23d7c3 authored over 2 years ago by Daniel Bryce <[email protected]>
www dir

661998bf48a9b48c5c5f61327a2f26045bea375d authored over 2 years ago by Daniel Bryce <[email protected]>
Update pages.yml

66cefe731d59551b5e6018a44bc04dc2c41e3a6c authored over 2 years ago by Daniel Bryce <[email protected]>
Create pages.yml

c8948191091106a9db551287155a4b6458e88c16 authored over 2 years ago by Daniel Bryce <[email protected]>
Update test file

eaca89063369e307f052183a466f642874ac8efb authored over 2 years ago by Bryan Bartley <[email protected]>
Cherry pick specialization from Friendzymes fork

8809072514b39b4407a6fb7543ce88e1c1b7d63d authored over 2 years ago by Bryan Bartley <[email protected]>
Fix bad uri

e5ad51118631019ede314a5b957084a20445bdb7 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix some broken lookups

e880051e9fe1822f4d365ae35ce9c35514395b8f authored over 2 years ago by Bryan Bartley <[email protected]>
PlateCoordinates now supports single well coordinate in addition to ranges

c38e6a6102f74616a7a6ffda5e3e32eef5aaae46 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge changes in compute_output method

c8af38209c7564f5a62e465f7f9d1d38c14d58c7 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix paml:contents specification

ac6dec9b3f79fc38c2b5f1a2a445e75e4e453068 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix test_subexecutions namespace error

345668667a2a0f32a4be61faf15045772183b76c authored over 2 years ago by Bryan Bartley <[email protected]>
Fix missing execution argument

2e8dd5a62045df141843a9e7d0a511aa7e6ce748 authored over 2 years ago by Bryan Bartley <[email protected]>
Fix test_subexecutions namespace error

0f4258fc4f23910ed6a3f0f206504c4a08d141bd authored over 2 years ago by Bryan Bartley <[email protected]>
Improve documentation of test cases

97aa8af33ceaa318d16d2dc291b6bcfd806ee1ef authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'main' into interlab_protocol

a1d4849f6a825c8de2518020fbdbc134ed1d1ec5 authored over 2 years ago by Bryan Bartley <[email protected]>
Correcte Exp3, made docx and PDF

54626a59df64a7ac4431ca80febdee86c83aa25d authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Check in markdown documents

6be0c6b00edd92bac3af844c02342f5de2933173 authored over 2 years ago by Bryan Bartley <[email protected]>
Specify missing protocol outputs

261a638d236a3eb2f89aa49f769b977e51ae2ddd authored over 2 years ago by Bryan Bartley <[email protected]>
Add debugging output

96cbf56bb0eb1454a167145cb8e1c70998634942 authored over 2 years ago by Bryan Bartley <[email protected]>
trying to make challenge work

c33e872f86f0ac4d08cba6f2e6325056e1d9849c authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Exp 1 and 2 MI, and some corrections

124f251e3412c5b4e9d2e8e92fd7ab9c5ac6b7be authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Merge branch 'interlab_protocol' of https://github.com/Bioprotocols/paml into interlab_protocol

ebc2ccc6bfface18ea5625b3eef5aa2f2bfa98b8 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Create Layout_Exp2.png

af816e4df7386bac67a6218d2e125f94a065091e authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Wrong fig corrected in Exp1

910f73d0a152149429e253f1fde9d6bccd7a3f01 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Corrected Exp1, and added Exp1MINI

7dfc1cda8e7b2c3b42b4dc09ab82acd5c8b1d92b authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Corrected J428106 in Exp1

cab20d3c79bae061ba6693d91778a2f446eaedd2 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Edited serial dilution image

bf0dd9d1b66c08a3523eeaf5b8207b180e22a549 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final versions for publish in web.

0ee39b240c9b76d8204fad11e6dcdc1685f8efda authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Updated Culture specialization to MD (overnight if hours > 14)

42b4e1905bcf85217a3a94f35e7fdf1ce0246d91 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final modifications

9cb052aede769f7edf38ec17c4d6ab745e6153e3 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
final touches to Standard exp3

e56497968fa8572320574a41dd12f12026e062b7 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Bump protocol version

a26041fb944c58de8cd15ac84e5b85429233f39f authored over 2 years ago by Bryan Bartley <[email protected]>
Add description

429cee27eac95e9f4e4a28c0ecc3430bba750b9c authored over 2 years ago by Bryan Bartley <[email protected]>
Add microplate seal to container ontologyand list it in the Materials section

01980313a1109605073fd7ca23b418925a684f05 authored over 2 years ago by Bryan Bartley <[email protected]>
Minor fix to protocol description

af66baf3b87066d6c2d30b65d9202fcae78f2840 authored over 2 years ago by Bryan Bartley <[email protected]>
Insert updated figures into Markdown document

0c59e411a2de09e5046dfc570ee7fc25d17468cf authored over 2 years ago by Bryan Bartley <[email protected]>
Some corrections to Exp1 Standard.

15ae41100d178e62982acd613a8f20689162701c authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Incorporate Traci's and Vinoo's suggested edits

e497203cdaf472df3dbcd05d0313d9fa7c6fc1ea authored over 2 years ago by Bryan Bartley <[email protected]>
Tweak Table title

d5c0cdaff0185a59d892b3d553bbc2528ddac896 authored over 2 years ago by Bryan Bartley <[email protected]>
List containers under Materials section of markdown document

df5f38cab9a55f51996032cd9ec17f2c3fbf7d6f authored over 2 years ago by Bryan Bartley <[email protected]>
Round rpm measures

f76e82f8f7d7d953ecffb938063477361a52c691 authored over 2 years ago by Bryan Bartley <[email protected]>
Change wording of provision primitives to be more readable

6bc1655783931d5a84ba2f099bc23e5d88db42a0 authored over 2 years ago by Bryan Bartley <[email protected]>
Support captions for embedded images

2a928c1c3892d9a0a1371392daa64db58785d631 authored over 2 years ago by Bryan Bartley <[email protected]>
Add HoldOnIce primitive

9a55cede9f61f44a95dc18556995096a93c5850a authored over 2 years ago by Bryan Bartley <[email protected]>
Version 1.1 of protocols, includes PickColony primitive

58db2c2c95a0dbd5fd8dab79187a46d59709d54a authored over 2 years ago by Bryan Bartley <[email protected]>
Add PickColony and CulturePlates primitives

1ffac44f2050d0aaa6fdb46913e858244908ea2c authored over 2 years ago by Bryan Bartley <[email protected]>
Update hyperlinks for some Components

ed69c4e1e3058be0d851c8db23a4d9c2dd28dffd authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

11a2f933b131ba09e80f1ab4c1c44532a95fcb7a authored over 2 years ago by Bryan Bartley <[email protected]>
Copy over exp1 and exp2 interlab protocols from Alejandro's branch

f7a3586c878af8bc39113c5fca8c783c2f2ca553 authored over 2 years ago by Bryan Bartley <[email protected]>
Update interlab-endpoint.py

98897e842075aefc48d5f073542c7380608bc867 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Move Outputs section of markdown document

1d1cb4cac813b30cc0ef446008bb2ecd15dee092 authored over 2 years ago by Bryan Bartley <[email protected]>
Add embedded image to markdown for multicolor particle calibration protocol

7afc9d266999adc7e1db886b31be53912ed580c0 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

f327385bacfeeb338ce9abadf668da182416d94a authored over 2 years ago by Bryan Bartley <[email protected]>
Insert reagent names into description text

e5dbf83f30a357f4719a3be299035a875f4dee72 authored over 2 years ago by Bryan Bartley <[email protected]>
Move markdown to Execution object instead of ExecutionEngine object

53921a20c7e601f838c2ca163bd7ba772932391a authored over 2 years ago by Bryan Bartley <[email protected]>
Bump protocol version

43fb5a87ccf7ce8e9eb247d6b4d13d9e31889299 authored over 2 years ago by Bryan Bartley <[email protected]>
Create serial_dilution.PNG

b12d548a9b42a90a90d7fea15e9d8d9786861001 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Check in markdown rendering for protocols as of now

00818e822fa662deadf7536a044e9f6fe6e6984e authored over 2 years ago by Bryan Bartley <[email protected]>
Render a table that shows where iGEM parts are located in the distribution kit

f8fb75b76d350de3979c5b36409a68657172c0e1 authored over 2 years ago by Bryan Bartley <[email protected]>
Scripts have been adjusted now that markdown is attached to Execution instances instead of the ExecutionEngine

d3930ed0ad20d21c065a8406a2685410b11d99c3 authored over 2 years ago by Bryan Bartley <[email protected]>
Add parts registry identifiers for test devices

952dcfa4935fcf1aa0c15b097775cee91eb26e0d authored over 2 years ago by Bryan Bartley <[email protected]>
Don't render section headers for empty sections

7a29adbc6d390e96b2ee28bcebc44d7c499552f0 authored over 2 years ago by Bryan Bartley <[email protected]>
Hack markdown rendering of Materials section

476730e0b0bc97980690afe3c6ceab6ae5930c02 authored over 2 years ago by Bryan Bartley <[email protected]>
Merge branch 'interlab_protocol' of github.com:Bioprotocols/paml into interlab_protocol

608b6fd7bbc478e4a132f326718c05593c58ba17 authored over 2 years ago by Bryan Bartley <[email protected]>
MarkdownSpecialization converts subprotocols into nested markdown rendering

5654fa2d0d7ddd4df3279dd34835753b05a97f77 authored over 2 years ago by Bryan Bartley <[email protected]>
typo

674b4cc4cf5568ef0ecf0626a007098b4da9fa68 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Updated well name to match 2022 distro plate 1.

a26b2c4d3247660aca5bd75b0841e71404ea3ae2 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Update revised-interlab-growth-curve.py

Updated, and modified the well location in the distribution

668c8780e2901b72c7b4849c70c3852671b046da authored over 2 years ago by Alejandro VIgnoni <[email protected]>
Update revised-interlab-growth-curve.py

b77f907c18615540400b2e9f257f8e6402e64cb7 authored over 2 years ago by Alejandro VIgnoni <[email protected]>
DefaultBehaviorSpecialization supports subprotocols

4f727f685ab569eb9483e0758c5759beca44079a authored over 2 years ago by Bryan Bartley <[email protected]>
Add specialized behaviors for subprotocols

f1e3e50936fbb44b37500df2832b416ebd0a69fe authored over 2 years ago by Bryan Bartley <[email protected]>
iGEM interlab examples

2bcde6500ab516f326df777249bc5fb471754f46 authored over 2 years ago by Bryan Bartley <[email protected]>
Add timepoints parameter to measurement primitives

84ea6906ba8f17af928c7d6301304c2f9b80b7aa authored over 2 years ago by Bryan Bartley <[email protected]>
Timepoint version of protocol

87ba6007644cc57d9fd29423b585616833640aa4 authored over 2 years ago by Bryan Bartley <[email protected]>
Incorporate feedback for the cell calibration protocol

f007d41404d9268438b964b0f5fd32314115e92e authored over 2 years ago by Bryan Bartley <[email protected]>
Merge pull request #140 from jamesscottbrown/patch-1

README: enable syntax highlighting

a1597f9e889be63a7cfb76f869224f200ca0e58f authored over 2 years ago by Daniel Bryce <[email protected]>
README: enable syntax highlighting

d08134410e5662f50fffe18b6a9bd82a5f31b81b authored over 2 years ago by James Scott-Brown <[email protected]>
Merge pull request #137 from Bioprotocols/xarrays-rebase

Xarrays rebase

802b65dc1628c53b149af47a525af8828ce516f5 authored over 2 years ago by bbartley <[email protected]>
fix error resolving literals

a8ca6a5680708534a8b8123a74424a3ac12b2940 authored over 2 years ago by Daniel Bryce <[email protected]>
represent arrays with serialized xarray

3b491ec331cf8ac3307787aff5cd58e92bf24f0d authored over 2 years ago by Daniel Bryce <[email protected]>
SampleArray and TransferByMap as Xarray

310196109af8b965a0d996cdaa7eb91897c23cfb authored over 2 years ago by Daniel Bryce <[email protected]>
added support for sample maps

54d3295f2080edf15dc515ba5600c0324c0ecb76 authored over 2 years ago by Daniel Bryce <[email protected]>
Convenience methods for getting active coordinates from a SampleArray/Mask

561452d4fce909277b83b248147877c5be6d9645 authored over 2 years ago by Bryan Bartley <[email protected]>