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github.com/Bioprotocols/labop

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

add new packages to setup.py

e1226217c720cdbc6698b35407bbaabec816e320 authored almost 2 years ago by Daniel Bryce <[email protected]>
refactor monkey patches into classes

72265c65917f3b8c522e25d74c8719cbca5196db authored almost 2 years ago by Daniel Bryce <[email protected]>
import sys

2d1f645e756e396c57cb50943618ce23b3c3999e authored almost 2 years ago by Daniel Bryce <[email protected]>
avoid timestamped test outputs

9d77d979f58503389f7c77f8dfc611d646b45986 authored almost 2 years ago by Daniel Bryce <[email protected]>
applied isort and pycln

868bef1598900d02da6d8aa451ff82675b364980 authored almost 2 years ago by Daniel Bryce <[email protected]>
add isort

4cce56e5a032ecdeaee59d90ec2c4fb8070b169b authored almost 2 years ago by Daniel Bryce <[email protected]>
formatted all source

c6087f6121e7c8c1cc02c0fb078e17e6302cb3f1 authored almost 2 years ago by Daniel Bryce <[email protected]>
import sorting and removal

5b53c902fb4b6c1f20539db4767f7638762c5ef6 authored almost 2 years ago by Daniel Bryce <[email protected]>
add black to pre-commit

673b49fe527cb33b7a7e634d69174a2bf9fff1cb authored almost 2 years ago by Daniel Bryce <[email protected]>
remove call to write data in notebooks

73cceb517f6ad0e1f81a15b5108ddd41db479892 authored almost 2 years ago by Daniel Bryce <[email protected]>
use relative path in test

ad882e0120640cfba721b486a3dd24acd00c0b63 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix output file naming and tests

3306466ce12e7295165f3f17d95aead13eba7a32 authored almost 2 years ago by Daniel Bryce <[email protected]>
sort ee choices for determinism

c0b9c837dda1fe19f82b0346c37fbfacade90f01 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests

9d81d47f781371e6c7a4c6dc461fb6a3d7208856 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix typing

f475dbf38cc129e27a0d0ef420781edb0e176efb authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests

d8700b702aa61f0f591a62d9d9ba7b4b5f255777 authored almost 2 years ago by Daniel Bryce <[email protected]>
add labop.utils to setup.py

1c658b2bd9a2769b40ef6b2bb1410dd0090ff649 authored almost 2 years ago by Daniel Bryce <[email protected]>
import utils package

6e4a1d9662b8b1e2e0fea254c7df915d863a40dd authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests

c1bf0c2017a96705e4db2ee1bc273c5bd984b207 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests, added stable hash for names

70e0886c7f7e76b2953e1ed7cde99311336c6230 authored almost 2 years ago by Daniel Bryce <[email protected]>
multicolor artifacts

c814c07c98350321f4394817aeadc769a85af031 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix md, xlsx humanizing, ee speedup

27f4dc9f7c260903085005b74d2c25de9cd52eeb authored almost 2 years ago by Daniel Bryce <[email protected]>
bad rebase saved and change md

2a4195717a30bba0d90a1181e135ae14d2a900ad authored almost 2 years ago by Daniel Bryce <[email protected]>
use a single data xlsx file

9a2ed696c3f39ca9e8eaf2ded06c4d18b00afa46 authored almost 2 years ago by Daniel Bryce <[email protected]>
dump sampledata template to xlsx

a8de7684ad423bf8e587f0a1d3c5b6c614586d3b authored almost 2 years ago by Daniel Bryce <[email protected]>
Get iGEM tests passing again

5f9b7e2f6431bc9798f281e0415674330642e1e1 authored almost 2 years ago by Bryan Bartley <[email protected]>
generated artifacts

6dc27c95c69401f373f9d16d0efea00d701897d5 authored almost 2 years ago by Daniel Bryce <[email protected]>
fixed up joining metada for multicolor protocol

c985eda2f20b425f1388ed0c264a9d09c156b37b authored almost 2 years ago by Daniel Bryce <[email protected]>
multi-color conver to xarray

e13b90d787e35712643fddded456c6057402b23a authored almost 2 years ago by Daniel Bryce <[email protected]>
multicolor as xarrays

e5e705f9587ced3d53b7034710a4432d267a3ab4 authored almost 2 years ago by Daniel Bryce <[email protected]>
Add hook to laboratory instrument readouts, generate simulated measurements

e01b94be06e27c71fbbeea9aa38768a8f7caa720 authored almost 2 years ago by Bryan Bartley <[email protected]>
Merge pull request #188 from Bioprotocols/readme

Readme

b3df6613fbcaae2e66797a6900cd3f55bef68019 authored almost 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #187 from Bioprotocols/remove-jetc-revert

Remove jetc revert

ad87538a6bcaac792b57b4f4899475dacb466328 authored almost 2 years ago by Daniel Bryce <[email protected]>
Fix misspelling

815ca3832d2af77dd9637d53705b9cb5b273cec3 authored almost 2 years ago by Bryan Bartley <[email protected]>
reorg data related instantiation/serialization

39d057ee6f0d8d1e5eca717e089fb9d2038b6cbd authored almost 2 years ago by Daniel Bryce <[email protected]>
address review comments

f69d885e217cebe1753a72fc94ed088bf4b1a0e1 authored almost 2 years ago by Daniel Bryce <[email protected]>
Update metadata for calibration protocol

4e92e3a5c6172cd4c55f87303eff14badba9bab7 authored almost 2 years ago by Bryan Bartley <[email protected]>
checkpoint, need to fix rebase first

362ea5670b79f485d78323fd80c3aed27dbe0180 authored almost 2 years ago by Daniel Bryce <[email protected]>
reference samplemetadata

980f98d21aa6b39b2b8377d815f985b69e0b4b22 authored almost 2 years ago by Daniel Bryce <[email protected]>
Implement ExcelMetadata primitive

cb36438bd6d5483e66262c05983aabd375944df1 authored almost 2 years ago by Bryan Bartley <[email protected]>
end to end metadata

f4511314ebf32131bef4285740d29f44885ba90a authored almost 2 years ago by Daniel Bryce <[email protected]>
small instance of calibration

0174d68eb8c3781acaddb9158d9b8754e8a3acf9 authored almost 2 years ago by Daniel Bryce <[email protected]>
Update labop/lib/sample_arrays.py

Co-authored-by: Jacob Beal <[email protected]>

2baa415d48bfd7479b4bb6a2fc3f46779dd39c77 authored almost 2 years ago by Daniel Bryce <[email protected]>
Added AttachMetadata primitive

65948e22ca9ea317967bc321fb8cdbb8623bcd53 authored almost 2 years ago by Daniel Bryce <[email protected]>
added creation of datasets

237a87060170f25560b92df78f9ed56fc8c36ab4 authored almost 2 years ago by Daniel Bryce <[email protected]>
changed measurements to output datasets

25f5cd187894654ae05f43e18d9dae2928bb15da authored almost 2 years ago by Daniel Bryce <[email protected]>
test case for joining metadata (broken)

5848f3e84391de650c228f27fccc54a32d2ca16d authored almost 2 years ago by Daniel Bryce <[email protected]>
copy error

f73502815e0b43b0337bc29b9439d02d67d1216a authored almost 2 years ago by Daniel Bryce <[email protected]>
Missing required caption

fc3f0ba26bd3458dde56412dd7b999338ded87eb authored almost 2 years ago by Daniel Bryce <[email protected]>
adjusted spec build instructions

ab17a8d01c6d41d78e0231ae71ffb1834302a60b authored almost 2 years ago by Daniel Bryce <[email protected]>
update spec build instructions

75006cd7e160b4d84ef40f90c9ebcd31318a24ac authored almost 2 years ago by Daniel Bryce <[email protected]>
fix rebase

15eee18f06542496a3f9654fac6a7607f248d6d2 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests

637f1c5901dd064063a1890f201ce6b29a627a77 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix rebase

57643a92ee573367b5b259040c2c893d0ead1b2a authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests, add more out dir usage

0b97f58478a9ca720cb4ccae4b129b906a7928a4 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests and add out dir for artifacts

6404640ce535600051c066aa5795d29a3685ee41 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix tests

dde4923988ec7841b5115cb6d8605291da75c23a authored almost 2 years ago by Daniel Bryce <[email protected]>
fix rebase

cb4a0398bbcac3e7d0e69f128293003573724df3 authored almost 2 years ago by Daniel Bryce <[email protected]>
remove imports

559cf71bec2c877e5b2550d65b87dbaa3935a111 authored almost 2 years ago by Daniel Bryce <[email protected]>
extend support for xarray sample arrays

b5c9d35b56b25df0af03dd9f53a457664b63915d authored almost 2 years ago by Daniel Bryce <[email protected]>
make matplotlib import only if plotting an xarray

9e13a6a3042288d09fa581506315b4f500441bc5 authored almost 2 years ago by Daniel Bryce <[email protected]>
handle transition

5cf7c3548e70072d701b1a27aa05acaaf6dee6a5 authored almost 2 years ago by Daniel Bryce <[email protected]>
record execution issues

0bd7a7a5c115d83acb79d076c1928c96ffa73524 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix finding token sources for transfer

9f11e6b9844bc9f0c265363247d471aa1127de4d authored almost 2 years ago by Daniel Bryce <[email protected]>
remove half-baked ee error handl.

28389e6965fa95c17aa6f0634e504183983f5693 authored almost 2 years ago by Daniel Bryce <[email protected]>
remove pytest dep

73da859abcafe67df9e98ed48641e5566c0e172a authored almost 2 years ago by Daniel Bryce <[email protected]>
remove paml-check submodule

a5d923a6f82ae439a2b1ce697deb35269ebb1205 authored almost 2 years ago by Daniel Bryce <[email protected]>
classes for execution issues

51ca4bda147108ae2c42ace1f9a9bd386dbf525c authored almost 2 years ago by Daniel Bryce <[email protected]>
missed in merge commit

22aea4e34107eb3f6eb270aea8b51dfbfe148910 authored almost 2 years ago by Daniel Bryce <[email protected]>
require all control tokens to enable activities

532ba4d3ad5bebdb8211169f57ce1aa5882cd805 authored almost 2 years ago by Daniel Bryce <[email protected]>
rebased ludox decision example branch on main

1269635ef5ed253300e09f0d3d5c3e9b65f5d228 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix final node enabled, graceful error in exec

2a129a774473f95c347aff6458edfd9f39daf088 authored almost 2 years ago by Daniel Bryce <[email protected]>
Added failure recovery to ludox protocol via a decision node.

09fc67641628eafc2975186ec3e0f7d56555ccd0 authored almost 2 years ago by Daniel Bryce <[email protected]>
added final node to protocol, and black formatting

d1a7245d691321bf78c4bda1e350836580f2497e authored almost 2 years ago by Daniel Bryce <[email protected]>
record execution issues

300a5c2bf5940b686e58e2df54de9148be8cba8d authored almost 2 years ago by Daniel Bryce <[email protected]>
classes for execution issues

d975b291c66accb99e8e27aa40f20ae67b87b0e6 authored almost 2 years ago by Daniel Bryce <[email protected]>
added graphviz to inspector

ecd5a55c6e4d47e08fee5aa3b46e7a302993b096 authored almost 2 years ago by Daniel Bryce <[email protected]>
fix finding token sources for transfer

aae748ee0d048137407e9b61904734d4fab457f2 authored almost 2 years ago by Daniel Bryce <[email protected]>
remove ipython dep in ee

7c561495c39da9026251774213a2b4dc10aee6f8 authored almost 2 years ago by Daniel Bryce <[email protected]>
added final node to protocol, and black formatting

32d968ed76468a683eebbb5c0e44c6a05dcbfed4 authored almost 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #184 from Bioprotocols/183-metadata-model

Propose SampleMetadata and Dataset classes

a6b31d7849afbca2aee9b0cce89fed1005d8768a authored almost 2 years ago by Daniel Bryce <[email protected]>
#183: change "labels" to "metadata"

7c8eb40ff060d82aa2f08c7b97274a4e51b6536b authored almost 2 years ago by Jake Beal <[email protected]>
183: update test .nt files to also use SampleArray.initial_contents instead of SampleArray.contents

5a72e1f8543cf223ce14304a67d3686ab7200e72 authored almost 2 years ago by Jake Beal <[email protected]>
183: change all references to SampleArray.contents to SampleArray.initial_contents

Note that a number of places in the markdown_specialization seem to be using it as a running mode...

e1be776498b9038b999fa1c059f57d633bc3bd5a authored almost 2 years ago by Jake Beal <[email protected]>
Address 183 by proposing SampleMetadata and Dataset classes, plus relabeling SampleArray.contents to SampleArray.initial_contents

aefa2fc6d5954ba8bcc3f6d25c641904104185c2 authored almost 2 years ago by Jake Beal <[email protected]>
Merge pull request #180 from Bioprotocols/jetc_revisions

JETC revisions

cc8d8f00506d504e9803f538ceb677d1651c8dba authored almost 2 years ago by bbartley <[email protected]>
Remove commented code

b9c81a7e3e58a0bd43da258c186a02e235f20e6c authored almost 2 years ago by Bryan Bartley <[email protected]>
Use tyto as a fallback to resolve container specifications when the container api is unavailable

ef55b5e72967bd4aa651ae1806b30937552bcb4e authored almost 2 years ago by Bryan Bartley <[email protected]>
Simple diff example for sorted N-triples

aa80961ea0a3923df7ebc6195d60db3ee3382f9a authored about 2 years ago by Bryan Bartley <[email protected]>
Tweak LUDOX_protocol to demonstrate versioning

5f38c1103b2a69f36c7fdf5de74814a48f5a0d42 authored about 2 years ago by Bryan Bartley <[email protected]>
Examples of version control / diffing

3777fe6b6f778c388a0b303a41304cf9fdd47803 authored about 2 years ago by Bryan Bartley <[email protected]>
Track version of Markdown document using git version tag

9f27697edafa61a2c35b1bab7353f91d85124e52 authored about 2 years ago by Bryan Bartley <[email protected]>
bump version

9ea0789e831404a54094a081204982bd73ae833b authored about 2 years ago by Daniel Bryce <[email protected]>
Update README.md

b4eb3e4d3125a94c30205ceeba426306c838d1fe authored about 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #173 from Bioprotocols/opentrons_pcr_example

Opentrons pcr example

dc2818a4b7baffcdd0c00b134a30c70d7e455dc5 authored about 2 years ago by Daniel Bryce <[email protected]>
Update test rubrics

74b5c9c1daf91b00a1d5450fd740c47ff21d0f3d authored about 2 years ago by Bryan Bartley <[email protected]>
When reading sample contents, don't choke when a well is empty

3c329378eb0c4a476b3c5188c4b516d3ba7ab656 authored about 2 years ago by Bryan Bartley <[email protected]>
Merge pull request #172 from Bioprotocols/opentrons-nb

Opentrons-nb

8968a0e26cc32d56d09c4f408ff4ad7a3bff51be authored about 2 years ago by bbartley <[email protected]>
Merge branch 'main' into opentrons-nb

3685fb7c987019edacf8c46d71098c35a94b3369 authored about 2 years ago by bbartley <[email protected]>
Extend compute_output handlers to handle different sample formats

d10a63d1a96040eac00bebf39bdf9d205f002f27 authored about 2 years ago by Bryan Bartley <[email protected]>