Bioprotocols Working Group commits | Ecosyste.ms: OpenCollective

Merge branch 'ecl' of https://github.com/Bioprotocols/labop into ecl

github.com/Bioprotocols/labop - be56f69145084c58449e6a5d4fa8872bc3e2dc80 authored over 1 year ago by Daniel Bryce <[email protected]>

remove units

github.com/Bioprotocols/labop - 0788076e959fc3e4f41602a838aa7b7e5b0a4dd9 authored over 1 year ago by Daniel Bryce <[email protected]>

When an ECL script is generated, wrap unit operations in a RoboticSamplePreparation object

github.com/Bioprotocols/labop - 1a558a168d65982237e36d7a1ca718a19d4555fd authored over 1 year ago by Bryan Bartley <[email protected]>

Merge branch 'ecl' of github.com:Bioprotocols/paml into ecl

github.com/Bioprotocols/labop - 3622d35cb4dc943bbd8b7ebdc12ef021ce9fd7cc authored over 1 year ago by Bryan Bartley <[email protected]>

Fix syntax error in generated ECL

github.com/Bioprotocols/labop - aca1dc064a8e5588655e2fe87be70fa7f807f920 authored over 1 year ago by Bryan Bartley <[email protected]>

Update python-package.yml

Remove python 3.7 build

github.com/Bioprotocols/labop - 9624acbc55aa68b8a0c44b0bcea7dd2191d7296a authored over 1 year ago by Daniel Bryce <[email protected]>

Update setup.py

github.com/Bioprotocols/labop - a9d0f84238a2dd8ce2e645a7fc09a3f4447a5ad3 authored over 1 year ago by Daniel Bryce <[email protected]>

Update setup.py

github.com/Bioprotocols/labop - 7ed69245caf1d27dbba3e53cbe3af64f1eb2ca9d authored over 1 year ago by Daniel Bryce <[email protected]>

Update setup.py

github.com/Bioprotocols/labop - 3e98bde173d2b983d23b58a248c1e31e720f2d23 authored over 1 year ago by Daniel Bryce <[email protected]>

Update pint version

github.com/Bioprotocols/labop - 04c939cda7cc5389ccd7988d668123c50b7cfbb7 authored over 1 year ago by Daniel Bryce <[email protected]>

upgrade pint dep

github.com/Bioprotocols/labop - 484d53ea7c314e26387492f5108e0f58692f0643 authored over 1 year ago by Daniel Bryce <[email protected]>

merge sample graph and ecl specialization

github.com/Bioprotocols/labop - 898ac33fd7e2d4bc2d7b81f371a748f8ad951938 authored over 1 year ago by Daniel Bryce <[email protected]>

Merge branch 'trajectory-jh' into ecl2

github.com/Bioprotocols/labop - ac097e6b3ef34f3548296fd5c3273738c0990fe2 authored over 1 year ago by Daniel Bryce <[email protected]>

modify for testing

github.com/Bioprotocols/labop - e79e4eb671e029859de478ff15d7a77d0eb2c71e authored over 1 year ago by Daniel Bryce <[email protected]>

fix sample id stability

github.com/Bioprotocols/labop - 5395ec2cf027616eaf8fbea0fb4795c6a7979ef2 authored over 1 year ago by Daniel Bryce <[email protected]>

add direction to serial dilution

github.com/Bioprotocols/labop - 63a65a6e2be6d4eaa6cee30854d04ea2bffde71a authored over 1 year ago by Daniel Bryce <[email protected]>

ordered samples

github.com/Bioprotocols/labop - deb55e1c5a35bf0175a2de5abbca433f0a2d6418 authored over 1 year ago by Daniel Bryce <[email protected]>

order samples support

github.com/Bioprotocols/labop - 0b757021333f2e8dc1148ab97c9cf4d55db82ca9 authored over 1 year ago by Daniel Bryce <[email protected]>

Add emerald cloud submodule to setup initialization

github.com/Bioprotocols/labop - d4bdf69e25c3cc43c327c0f928aa574b3d6c7b4f authored over 1 year ago by Bryan Bartley <[email protected]>

Improve container resolution

github.com/Bioprotocols/labop - f26ac5a119818976e3456674e39a9d686843f5c7 authored over 1 year ago by Bryan Bartley <[email protected]>

Clean out old opentrons stuff

github.com/Bioprotocols/labop - 5c8f8787fb63be1cf1904d57197b56251084d190 authored over 1 year ago by Bryan Bartley <[email protected]>

Generate Emerald Cloud multicolor calibration protocol

github.com/Bioprotocols/labop - a7a55c074ce02834e86f113c9f890cdd5d57b466 authored over 1 year ago by Bryan Bartley <[email protected]>

Remove debugging output

github.com/Bioprotocols/labop - 8b340e7662d8e2cb96412a6bb8db3086c9869e32 authored over 1 year ago by Bryan Bartley <[email protected]>

Clean up container resolution

github.com/Bioprotocols/labop - 75202b96a0fc379816b20cc438f59ddc51f31110 authored over 1 year ago by Bryan Bartley <[email protected]>

import fix

github.com/Bioprotocols/labop - c2020e43b93ffb5b87bffbb531d600000fa94e43 authored over 1 year ago by Daniel Bryce <[email protected]>

ecl package

github.com/Bioprotocols/labop - 5c075cda0b54a5f89388eadb99f133159443e25b authored over 1 year ago by Daniel Bryce <[email protected]>

remove networkx dep

github.com/Bioprotocols/labop - 8a3a7bb1519351c24446308b83e3aae7cfc575bc authored over 1 year ago by Daniel Bryce <[email protected]>

Merge branch 'ecl-db' into trajectory-jh

github.com/Bioprotocols/labop - cf92f4c57d7d12f6a80a7b4e89304a41b18ce37b authored over 1 year ago by Daniel Bryce <[email protected]>

order locations primitive and ecl script

github.com/Bioprotocols/labop - 0811290a0cbb1748ce941de0d39076aebcfabb58 authored over 1 year ago by Daniel Bryce <[email protected]>

Fix uninitialized link between SampleArray and its ContainerSpec

github.com/Bioprotocols/labop - 914ec60475d3e56aafd78d6a72af334fc64a55c2 authored over 1 year ago by Bryan Bartley <[email protected]>

almost all tests

github.com/Bioprotocols/labop - 559c50b358e8d7e893af1a631013da271d1834ad authored over 1 year ago by Daniel Bryce <[email protected]>

Add some more microfuge tubes to container ontology

github.com/Bioprotocols/labop - 2d4ea03e97b1fa5e902b2ecf12ec9f7b3affe77a authored over 1 year ago by Bryan Bartley <[email protected]>

fix tests

github.com/Bioprotocols/labop - ced89e89f93965c37940fbe56f392c0246a50fef authored over 1 year ago by Daniel Bryce <[email protected]>

finished sample graph feature

github.com/Bioprotocols/labop - 702bf26c2a854e940d35f200f9edc7d2d615fd08 authored over 1 year ago by Daniel Bryce <[email protected]>

working sample graph minus serialdilute

github.com/Bioprotocols/labop - c278c0b4977a4e0fd861730255d598e1c54cfcf4 authored over 1 year ago by Daniel Bryce <[email protected]>

Fixing tests

github.com/Bioprotocols/labop - 1df5cd4ac5e29d3817d8059cd1d87b7566765f81 authored over 1 year ago by Daniel Bryce <[email protected]>

WIP for getting trajectory to work with multicolor calibration

github.com/Bioprotocols/labop - ddf2928821c52fe62f5bff2f3a16c20ec1eae345 authored over 1 year ago by John Harwell <[email protected]>

Add method for turning a coordinate rectangle into a flat list of indices

github.com/Bioprotocols/labop - fa793615721025d6d81446fa96818368f7723c60 authored over 1 year ago by Bryan Bartley <[email protected]>

Initialize submodule for Emerald Cloud specialization

github.com/Bioprotocols/labop - 721202d2fefa0785d52f6e75b69621d1a40736fc authored over 1 year ago by Bryan Bartley <[email protected]>

setup trajectory computation by default

github.com/Bioprotocols/labop - 789e9815f05712193490b874f13d00d4c4c8a57d authored over 1 year ago by Daniel Bryce <[email protected]>

feature: Sample provenance observer

- More robust flowing from sources -> targets for TransferByMap
- Workaround bug in sbolfactory ...

github.com/Bioprotocols/labop - b6a35faf4883ebcf0461521682a3e5cf547953a1 authored over 1 year ago by John Harwell <[email protected]>

Setup state trajectory record

github.com/Bioprotocols/labop - 0cbf64038dbf1571f22e4cabecfc4b040b1c1ce2 authored over 1 year ago by Daniel Bryce <[email protected]>

feature: Sample provenance observer

- Only works for TransferByMap operations; others to be added as needed.

github.com/Bioprotocols/labop - 77b182976a55cc490ef06cd41293482cb0d10353 authored over 1 year ago by Daniel Bryce <[email protected]>

added final node to protocol, and black formatting

github.com/Bioprotocols/labop - b43e7447381621657b8021ee4439ca5667be3e03 authored over 1 year ago by Daniel Bryce <[email protected]>

Add some more docstrings to sample provenance graph module

github.com/Bioprotocols/labop - 96c5274bdeb74ed8af717b23606ecd70affb8fd7 authored over 1 year ago by John Harwell <[email protected]>

gathered all edges and new samples in dataset

github.com/Bioprotocols/labop - b9d3bf21a288a66ea9b92d8512b3f08bead10a86 authored over 1 year ago by Daniel Bryce <[email protected]>

feature: Sample provenance observer

- Only works for TransferByMap operations; others to be added as needed.

github.com/Bioprotocols/labop - 7fcad15f62c56418096e8b7f500ab2583811cc95 authored over 1 year ago by Daniel Bryce <[email protected]>

feature: Sample provenance observer

- Start switching to xarray from networkx
- I have something that runs and doesn't crash, and se...

github.com/Bioprotocols/labop - 41cad25bf7bdbf659ae83393131bb42069d8585c authored over 1 year ago by John Harwell <[email protected]>

clean up sample array init and transfer

github.com/Bioprotocols/labop - 1ac9eace5c08594f0fb989d928cf06227b5081a2 authored over 1 year ago by Daniel Bryce <[email protected]>

working computation of transfer map, code broken

github.com/Bioprotocols/labop - b1488ae72418b9cb6916a42742c6f1037d840e03 authored over 1 year ago by Daniel Bryce <[email protected]>

xarray graph test case

github.com/Bioprotocols/labop - 09b4225dee1e2b0ff3d0c2f4db71eb232f825a40 authored over 1 year ago by Daniel Bryce <[email protected]>

handle transition

github.com/Bioprotocols/labop - 1ff3406675392c109bbc7799f3006c4a81576b3d authored over 1 year ago by Daniel Bryce <[email protected]>

extend support for xarray sample arrays

github.com/Bioprotocols/labop - d6adc607d98071d93eaa7ff7c93e5df71908c285 authored over 1 year ago by Daniel Bryce <[email protected]>

fixed/simplified transfer computation

github.com/Bioprotocols/labop - e2896099ca24dcc1639eaedddeee19ea116eb61c authored over 1 year ago by Daniel Bryce <[email protected]>

fix tests and add out dir for artifacts

github.com/Bioprotocols/labop - dbce24f2c2260701148c5174fc1a935f87c58de7 authored over 1 year ago by Daniel Bryce <[email protected]>

fixed string

github.com/Bioprotocols/labop - ce9786d2be1d03810b4717d660ef55dfd8da2980 authored over 1 year ago by Daniel Bryce <[email protected]>

Revert "JETC revisions"

github.com/Bioprotocols/labop - b24904523a8fd210a30a62a3ccde795a50a4c665 authored over 1 year ago by bbartley <[email protected]>

record execution issues

github.com/Bioprotocols/labop - 93eccc0bf3d16e1205d99bbabf12efa57b7c5e14 authored over 1 year ago by Daniel Bryce <[email protected]>

feature: Sample provenance observer

- More robust flowing from sources -> targets for TransferByMap
- Workaround bug in sbolfactory ...

github.com/Bioprotocols/labop - 8c294925a31d36474488b3881bcf57f66a9d0b34 authored over 1 year ago by John Harwell <[email protected]>

components of sample graph

github.com/Bioprotocols/labop - 647f26a8fcc55477ffd0387b97c0a64caae57add authored over 1 year ago by Daniel Bryce <[email protected]>

Setup state trajectory record

github.com/Bioprotocols/labop - 18e61f2c78ff4ac3c8230d0c26a52b10297ba2a6 authored over 1 year ago by Daniel Bryce <[email protected]>

static well formedness check

github.com/Bioprotocols/labop - d2ed261911288716831bb4596199eab398f7436c authored over 1 year ago by Daniel Bryce <[email protected]>

working example, tests failing still

github.com/Bioprotocols/labop - 083345f1aa1b901b096e0977230a6f4e3a6d3227 authored over 1 year ago by Daniel Bryce <[email protected]>

progress on next_tokens

github.com/Bioprotocols/labop - 45caefab883095cfafd364be82ac32050b6a24a9 authored over 1 year ago by Daniel Bryce <[email protected]>

Merge pull request #194 from Bioprotocols:update_autoprotocol

Update_autoprotocol

github.com/Bioprotocols/labop - 820c92eca815c480d507c55ac0fdb7c0dd39297e authored over 1 year ago by Daniel Bryce <[email protected]>

finalized version ready for pr

github.com/Bioprotocols/labop - 87f9d31e67d6d31246120712044152d4abc5079e authored over 1 year ago by Daniel Bryce <[email protected]>

fixed a couple tests

github.com/Bioprotocols/labop - 19e009a98f210f03130029c39390a9021660d447 authored over 1 year ago by Daniel Bryce <[email protected]>

use discard container

github.com/Bioprotocols/labop - e4f6f35bce765532e015bc072bd1575d315d5d77 authored over 1 year ago by Daniel Bryce <[email protected]>

autogen md.pdf if pandoc

github.com/Bioprotocols/labop - 86cb6c2eeafdd8c74590c5ccbef7f44c622b5a91 authored over 1 year ago by Daniel Bryce <[email protected]>

clean up merge

github.com/Bioprotocols/labop - 57a5f0a9dbe11cb3572d3153ffed343e8ba5185f authored over 1 year ago by Daniel Bryce <[email protected]>

Merge remote-tracking branch 'origin/main' into update_autoprotocol

github.com/Bioprotocols/labop - 9ad376adff4efa1a75be0163f65e13dad1f0f703 authored over 1 year ago by Daniel Bryce <[email protected]>

update script for md and autoprotocol

github.com/Bioprotocols/labop - 8e699133efffc3c8c0ff5f0b7db2e4bc16a657bd authored over 1 year ago by Daniel Bryce <[email protected]>

updated reagent components

github.com/Bioprotocols/labop - f605982638c0a75ffbbb4d7bca7754bf50de1b8e authored over 1 year ago by Daniel Bryce <[email protected]>

Implement SerialDilution primitive

github.com/Bioprotocols/labop - 0907f297b67c3366664b6e4bbd9c0ebca6b2f7ec authored over 1 year ago by Bryan Bartley <[email protected]>

checkpoint

github.com/Bioprotocols/labop - da9296c63ef24845fb9f76e15ee8ac57a7c0d11f authored over 1 year ago by Daniel Bryce <[email protected]>

Update protocol to support Autoprotocol conversion

github.com/Bioprotocols/labop - 8eb34378fa90b530ded757524bba5e6ebeeb00db authored over 1 year ago by Bryan Bartley <[email protected]>

Remove output pin from Vortex Primitive

github.com/Bioprotocols/labop - 15276d72cbae0d635282fa25aa4b9148c3ad7c1e authored over 1 year ago by Bryan Bartley <[email protected]>

Update to use new convenience methods for sample coordinates

github.com/Bioprotocols/labop - 51ea93fbf08803e55db9cbf073c747902bbef0fe authored over 1 year ago by Bryan Bartley <[email protected]>

Return coordinates as rect instead of list

github.com/Bioprotocols/labop - d410f699be1f702292a59038772fe714094cebf9 authored over 1 year ago by Bryan Bartley <[email protected]>

Merge pull request #193 from Bioprotocols:calibration-update

removed diluent clause

github.com/Bioprotocols/labop - 3cac677629b87522b295658a360168506558aee3 authored over 1 year ago by Daniel Bryce <[email protected]>

removed diluent clause

github.com/Bioprotocols/labop - 5c6b345420c4cca97e1121ead00812eb6d5e2ec3 authored over 1 year ago by Daniel Bryce <[email protected]>

get_value setup

github.com/Bioprotocols/labop - d8c48be1b8d1bd23e66dc6838aa3f08301294852 authored over 1 year ago by Daniel Bryce <[email protected]>

Merge pull request #192 from Bioprotocols/calibration-update

Calibration-update

github.com/Bioprotocols/labop - 7a73b0c91e89a9fcee44745c46071bcb40b01c04 authored over 1 year ago by bbartley <[email protected]>

Use uuid to generate unique autoprotocol datarefs

github.com/Bioprotocols/labop - adf045520568377beced7bfff42d006f65dcc872 authored over 1 year ago by Bryan Bartley <[email protected]>

md pdf

github.com/Bioprotocols/labop - b2083712edbd839e80eb83679b2a36dc1f066412 authored over 1 year ago by Daniel Bryce <[email protected]>

fixed serial dilution string

github.com/Bioprotocols/labop - 7462909baaf27c1ac58bc0615289c63ce97e0028 authored over 1 year ago by Daniel Bryce <[email protected]>

gen md.pdf

github.com/Bioprotocols/labop - bc101be590a56004340df5658dc558b70b3b5fa3 authored over 1 year ago by Daniel Bryce <[email protected]>

adjust protocol

github.com/Bioprotocols/labop - 18929bbefc4fc4ff29b48f5817c88158f4b448b6 authored over 1 year ago by Daniel Bryce <[email protected]>

setup execution context based exec

github.com/Bioprotocols/labop - a1702b0e38f3c1cfe3ddbffad51eb7e3d4a7bf40 authored over 1 year ago by Daniel Bryce <[email protected]>

added execution_context to manage call stack

github.com/Bioprotocols/labop - a219033358f3be582bb966cbc61e285094a78b09 authored over 1 year ago by Daniel Bryce <[email protected]>

Support more Strateos container types

github.com/Bioprotocols/labop - 1cbdb2aa2a9a113e18128186137e04271d741572 authored over 1 year ago by Bryan Bartley <[email protected]>

Merge pull request #191 from Bioprotocols/multicolor-md-fix

Adds more robust handling of coordinates to markdown specialization

github.com/Bioprotocols/labop - b0a6124f813721d916489f5d7ae122b3b2316b77 authored over 1 year ago by Daniel Bryce <[email protected]>

fix md output for bbartley comments

github.com/Bioprotocols/labop - 29155df0529d295daac0307aa17a01078b148320 authored over 1 year ago by Daniel Bryce <[email protected]>

fix wells in md

github.com/Bioprotocols/labop - cd8111b6ae389b93dc1269c12de489f056eedc75 authored almost 2 years ago by Daniel Bryce <[email protected]>

broken state of refactoring ee

github.com/Bioprotocols/labop - 7db2c40029eb6e71cacde1552cb5ecf771e1286a authored almost 2 years ago by Daniel Bryce <[email protected]>

rearrange imports

github.com/Bioprotocols/labop - 964840cb3e5619b0217e6290358e8a8c971f9727 authored almost 2 years ago by Daniel Bryce <[email protected]>

Reenable autoprotocol test and bring up to date with current execution engine

github.com/Bioprotocols/labop - a87f3c42eb6ade55c9dee418574883740d03be8d authored almost 2 years ago by Bryan Bartley <[email protected]>

added builders that use outer classes

github.com/Bioprotocols/labop - 0237daac4cc3d8d419d98edb86c6e247fa83bbd2 authored almost 2 years ago by Daniel Bryce <[email protected]>

Merge pull request #190 from Bioprotocols/black-pre-commit

Black pre commit

github.com/Bioprotocols/labop - 16da678e58fbf66103fa3ad49d4963b17b85c8fc authored almost 2 years ago by Daniel Bryce <[email protected]>

Merge pull request #189 from Bioprotocols/calibration-data-rebase

Automated Dataset Generation

github.com/Bioprotocols/labop - 3361294af1c552e2a9ce97cfddd76fa222913ca1 authored almost 2 years ago by Daniel Bryce <[email protected]>