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github.com/Bioprotocols/labop

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

Update github workflow to install optional paml-check

f2cc3977d65492aa30a45129ff63231dd0a20251 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge branch 'main' into 78-upgrade_rdflib

aab17a8538a2b44546b1170ad95440a29c6a1a49 authored almost 3 years ago by Bryan Bartley <[email protected]>
Replace opil:compositionalProperty with sbol:directlyComprises

529d118b5dfb27dfd225c8522e0d140c9ae8b2c4 authored almost 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #85 from Bioprotocols/81-paml_check

Move paml-check to optional requirements

f8b9a0357527ef18e04372e5ad5cf7ca78bd5e8d authored almost 3 years ago by bbartley <[email protected]>
Move paml-check to optional requirements

666f68149d40855f3cc0ee91c235d2bb57a62b12 authored almost 3 years ago by Bryan Bartley <[email protected]>
Add "no-clone" pip install instructions.

`pip` can install with a git URL as argument.

99ea91857547fb129391b52d07d752a9dbe2693c authored about 3 years ago by rpgoldman <[email protected]>
Update README.md

8155a2a6eebedf26fc6f97c0bcdab8fa7080f805 authored about 3 years ago by Jacob Beal <[email protected]>
Temporarily downgrade RDF-related dependencies (#82)

Fix the GitHub CI by avoiding RDFLIB 6-related issues

d030b266338aaeebfe6a9bda140bd8258bfa0aea authored about 3 years ago by rpgoldman <[email protected]>
Debug

31066f6b1718c304477ee58b98a4049f6c37e062 authored about 3 years ago by Bryan Bartley <[email protected]>
Upgrade pysbol and sbol_factory dependency

55bf90296a54cb6001b47ba0d649cca939a4441d authored about 3 years ago by Bryan Bartley <[email protected]>
Upgrade rdflib dependency

398085839cb6176fb403c722461a9adea9199b9c authored about 3 years ago by Bryan Bartley <[email protected]>
Merge pull request #73 from Bioprotocols/interactive-notebook-readme

Update README.md

60064fc82d4c911d2c39e7f4b33862ee4f4c0c83 authored about 3 years ago by Daniel Bryce <[email protected]>
Update README.md

ef4be6779c2166713b7d624980edd167a3cdc4b6 authored about 3 years ago by Daniel Bryce <[email protected]>
Update README.md

c4b97659909b50e4689928b2ae820bc4f92f1a74 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #65 from Bioprotocols/to-autoprotocol

This branch adds functionality to output different "specializations" of a protocol to either mar...

ac03faf1cfdf29fa4a9a72753454f718598a8a83 authored about 3 years ago by Daniel Bryce <[email protected]>
undo github action to run specific notebooks

939b108b437f624302b090ea1601a8d9a5bfaa09 authored about 3 years ago by Daniel Bryce <[email protected]>
use github action to run specific notebooks

ac29b6a7c66203cfb6f0d01a9380e97d946e4f24 authored about 3 years ago by Daniel Bryce <[email protected]>
use github action to run specific notebooks

779ef7e62ec577346c961199971955a41ee5ce3f authored about 3 years ago by Daniel Bryce <[email protected]>
install paml-check dep

e40e0da2cc93632161bb162470d21fc5496ee5b3 authored about 3 years ago by Daniel Bryce <[email protected]>
install paml-check dep

20f213e63e3504f49318d38f8fa4a35ddf1113f2 authored about 3 years ago by Daniel Bryce <[email protected]>
use default env for notebooks

8c072a7daefd2716122c2ba113b17018c2ce7778 authored about 3 years ago by Daniel Bryce <[email protected]>
install test dependencies for pytest

2c70725bb9617323d12f8ca1f920b41c14f71172 authored about 3 years ago by Daniel Bryce <[email protected]>
install test dependencies for pytest

51610f5b00263548b6df9303dda4a031e0bee95b authored about 3 years ago by Daniel Bryce <[email protected]>
merge request cleanups and notebook testing enabled in github

39048beddb990afad69e929d88622bd0d40dce6f authored about 3 years ago by Daniel Bryce <[email protected]>
Added Notebook tests and pre-commit hooks for removing notebook output and some other source checks.

01f4d76ce9073c41ae4daa16a975408cb77b128a authored about 3 years ago by Daniel Bryce <[email protected]>
using ordered parameters for execution, but still getting non-deterministic output.

5482a9d24e462d955dcd3829b3360e10cd48a3ac authored about 3 years ago by Daniel Bryce <[email protected]>
prepared notebooks for test.

3052e4558f59ff5b9f0ad71c6d03d2fbcf1ae042 authored about 3 years ago by Daniel Bryce <[email protected]>
Propagated change to using LiteralReference for EE values into the conversion output formats.

27b052c4aa053ddd277d599a63bc8830c5b57f2e authored about 3 years ago by Daniel Bryce <[email protected]>
Added Strateos instructions to README. Modified references to Transcriptic to be Strateos.

d2e76b3ed97e273595fca7286e967095675565b9 authored about 3 years ago by Daniel Bryce <[email protected]>
Add executable scripts.

Added `restrictions` and `to_sorted_ntriples` scripts to be installed with pip install. These ma...

a2ddb7b1332ef0af5fa74bd9d6da189cc326b617 authored about 3 years ago by Robert P. Goldman <[email protected]>
use more supported version of dict merge

eb891fcde5471ed8cdfde679a5f400df00eae648 authored about 3 years ago by Daniel Bryce <[email protected]>
fixed references to call parameter values

1eaf23eb16b1b008251748e8a65b4cb0a5d9382f authored about 3 years ago by Daniel Bryce <[email protected]>
Restore old TTL files.

4ecbf9a52467557db749a4589a7c0233b23f80f6 authored about 3 years ago by Robert P. Goldman <[email protected]>
Fixes to OWL RDF utils.

Another fix.

c9e7e2a9ae01f0964a1dac1c213025b1ea1b7c70 authored about 3 years ago by Robert P. Goldman <[email protected]>
Add owl_rdf_utils module.

This contains code for handling bad restrictions and code for translating a graph into sorted nt...

51b2dec57d3de74fc54e12e052846ebe87db23c4 authored about 3 years ago by Robert P. Goldman <[email protected]>
Correct the installation information in README.txt

Corrected the installation information in README, also adapted basic API docs

d6b457dd47d835a5bc34c22f78c2764dffde29a0 authored about 3 years ago by Jacob Beal <[email protected]>
Fix the malformed OWL restrictions.

Add Jupyter notebook with the code for finding and fixing ill-formed
owl:Restriction definitions...

36136cce296c69cba7b8ae7b21eb50c419908375 authored about 3 years ago by Robert P. Goldman <[email protected]>
added ipython dep

25b871427c32d5cd39412d3f57bea547814906f5 authored about 3 years ago by Daniel Bryce <[email protected]>
fix container ontology dep

a9dccb1eea93f8830e3f6fecbf88ec56818c937c authored about 3 years ago by Daniel Bryce <[email protected]>
Typing hint was wrong type

8d5725a53ab1cc5172e41ed4a0b675654a711def authored about 3 years ago by Daniel Bryce <[email protected]>
demo notebook with output.

b9016eb9bc3786c5d4b2c92ede818e92dbe6edaf authored about 3 years ago by Daniel Bryce <[email protected]>
demo notebook with output.

112cfe9c64badcf292baf6cc85bb120efe812a9c authored about 3 years ago by Daniel Bryce <[email protected]>
notebook README.md

436c31bbc1cb9808aa818390d59a888b20b8bb25 authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

2781fc5a74189476a4a1e6363373335ecec7368b authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

97504b1f60d8bc47a9f4425b473d3d6c6d32beb4 authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

e87c1ffa4fec4f3c62d2c6dbab3546f41814619a authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

30a33980e92fc42aaa30ef9fdcd8c6cc159b907b authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

43f9561154f55340bf2374df13c24a87416ca8db authored about 3 years ago by Daniel Bryce <[email protected]>
add deps for tests

b73240cdc6ae3fbb47e914599071a5fcb0e1433b authored about 3 years ago by Daniel Bryce <[email protected]>
demo final

4b1e6063ac94afc1209d5c54b36543aba45be8a9 authored about 3 years ago by Daniel Bryce <[email protected]>
stable demo code. still cleaning up notebooks.

6da58d8e15e4c5f3208cec47f3813fcaf3b5ae6b authored about 3 years ago by Daniel Bryce <[email protected]>
validation failing on execution, but bypassing

6fa6b6774354bb2ff10b8d3867684815b44780c1 authored about 3 years ago by Daniel Bryce <[email protected]>
fixed failing tests

59d86bc26630a3f95d3e290a8b9b34069f5a029d authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint on markdown conversion

724cf21c8e291960015247edccee32709569fdf3 authored about 3 years ago by Daniel Bryce <[email protected]>
Autoprotocol done

174bdf6394600d983c67d8bdc1edd526ec4e521c authored about 3 years ago by Daniel Bryce <[email protected]>
working container resolution through container ontology.

a22617c86e13eef27de1d3ca9ddd0bbdc47c3d44 authored about 3 years ago by Daniel Bryce <[email protected]>
remove markdown test and testing container creation

075b9ea0262628f5ca092366b96de73d9429cc71 authored about 3 years ago by Daniel Bryce <[email protected]>
started markdown specialization

66506b46ed05ffeeb986719d28ad4e57812e16e0 authored about 3 years ago by Daniel Bryce <[email protected]>
started markdown specialization

ebba1e84e0568af7335dad797b7fecf92639d171 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge branch 'markdown' into to-autoprotocol

05669d99543d624db113d4020f5ef8cfa20dc85b authored about 3 years ago by Daniel Bryce <[email protected]>
notebook for autoprotocol conversion demo

397a6857e45b150b12851491e6a7a104223c53eb authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint on conversion, needing uri resolution against Strateos

724841b59eb6a6b8b9d27ad7b71a90498779864b authored about 3 years ago by Daniel Bryce <[email protected]>
add logger

f1d11180e7dabc29b983003489988e205e1bde1b authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint on conversion, needing uri resolution against Strateos

86b6a37b32dc294acc4f4619d861cb2ac7cf3d18 authored about 3 years ago by Daniel Bryce <[email protected]>
get existing container from inventory by query on type

913fb9b669c4f832611cfae52dc34b2f5d8c5894 authored about 3 years ago by Daniel Bryce <[email protected]>
checkpoint on conversion, needing uri resolution against Strateos

564e5723396c302ad5227e3a956528bde37680af authored about 3 years ago by Daniel Bryce <[email protected]>
initial prototyping of execution to autoprotocol

4d1aaf2b4f9ae6a09d2b0688e1e29ec451d44bbe authored about 3 years ago by Jack Ladwig <[email protected]>
add ipython dep

07503c6132a11241ac7eef3414bf6c6a6b1b377b authored about 3 years ago by Daniel Bryce <[email protected]>
reviving markdown with basic functionality

8d42ffcaeb2dc0f13e394f363f23a9a94252c63e authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #61 from rpgoldman/revise-imports

0ef8dbc5e110890d09567f083fd162064f9b7189 authored about 3 years ago by rpgoldman <[email protected]>
Update README.md

278d86dbbc7cb268fdf288995f81478a0176b867 authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #62 from SD2E/cleanup

WIP: Cleanup

9015e97c7cd87f7fbf18aa4c1deb9ac6eeb8fcdb authored about 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #64 from SD2E/demo

Demo

74483b62ce96e212055d931a980f0b5e6cb8d2e1 authored about 3 years ago by Daniel Bryce <[email protected]>
removed rdflib-jsonld

531112681bc50776ea54873270289bc9d3d27762 authored about 3 years ago by Daniel Bryce <[email protected]>
refactored spec building and added to readme

updated dep versions in setup.py

9593c56cfe52138e3ea90d68c8149771edea2a7d authored about 3 years ago by Daniel Bryce <[email protected]>
refined demo notebook and made legend optional for plotting.

3a3f0bd82af9ce743841eeadaf3f0a4f240f7f7e authored about 3 years ago by Daniel Bryce <[email protected]>
ignores

fedd0b746af103215fc69e06194d0b2d913ab134 authored about 3 years ago by Daniel Bryce <[email protected]>
Move content from top level to subdirs. Remove output files from top level.

80db6a989c7d09476ca7d91b47b8198a605ff352 authored about 3 years ago by Daniel Bryce <[email protected]>
modify plotting for demo

0bb820a3d6b436b570e45e5655d4206f894e5f90 authored about 3 years ago by Daniel Bryce <[email protected]>
Remove definitions of owl properties.

`owl:minCardinality` and `owl:maxCardinality` are defined as `owl:AnnotationProperty`'s in uml.t...

d48ed57aad15db9000a2e77bd1fd8545a97ee215 authored about 3 years ago by Robert P. Goldman <[email protected]>
Modify imports.

Replace use of prefix IRIs with ontology IRIs in `owl:imports`.

0cbe8240cc153a468297a7842e53c6bbb0a65593 authored about 3 years ago by Robert P. Goldman <[email protected]>
Merge pull request #57 from SD2E/model-comments

Add descriptions for SampleCollection, SampleData, and ContainerSpec.

ca50d5c516ff6660e19e3a8cd59cbee4d0c2d03c authored about 3 years ago by Jacob Beal <[email protected]>
Update generator script for latest version of sbol_factory

01db0d76f52f6fb2cc423578b6fa8860cefb817d authored about 3 years ago by Jake Beal <[email protected]>
Add script for generating specification content, assuming that PAML and PAML-specification are sibling directories on Mac or Unix.

ff85b63217c8c51ff814cc55eba9ebd98e172ac1 authored about 3 years ago by Jake Beal <[email protected]>
Add descriptions for SampleCollection, SampleData, and ContainerSpec.

First pass on PAML descriptions is complete.

c7bfefcf2fd2737d63c042248a01b2d2bf42ffdb authored about 3 years ago by Jake Beal <[email protected]>
Merge pull request #56 from SD2E/model-descriptions

Model descriptions

7d811e40863fdc1299dea828aa8cc918bea7a1d0 authored about 3 years ago by bbartley <[email protected]>
Add descriptions for ActivityNodeExecution and CallBehaviorExecution

3614c31ee3010fcbba36f296ac63b62b2f5d8147 authored about 3 years ago by Jake Beal <[email protected]>
Merge commit '5381793c094143443d7e7005ca4b2f0b2d6fe373' into model-descriptions

38657cdecfc9238e1283e0e70daeedab3b2f0d6c authored about 3 years ago by Jake Beal <[email protected]>
Merge pull request #55 from SD2E/uml_documentation

Add documentation to UML ontology using rdfs:comment

5381793c094143443d7e7005ca4b2f0b2d6fe373 authored about 3 years ago by bbartley <[email protected]>
Add documentation to UML ontology using rdfs:comment

dadd1d166fc5a09adfd5b92abfce5e5c239052f1 authored about 3 years ago by Bryan Bartley <[email protected]>
Improve description of BehaviorExecution, add descriptions for Material, ProtocolExecution, and ActivityEdgeFlow

f6edc0c4cd0c3eb2c25a6ea51c04f358d8466c02 authored about 3 years ago by Jake Beal <[email protected]>
Full specification comments for PAML classes Protocol, Primitive, BehaviorExecution, and ParameterValue

608bf2b46797b2aca1bf6074d162aea88671ae87 authored over 3 years ago by Jake Beal <[email protected]>
Merge pull request #49 from SD2E/notebooks

Notebooks

8f9018927d114231eb8013fd848848af9ee2eb5d authored over 3 years ago by Daniel Bryce <[email protected]>
Merge branch 'main' into notebooks

0c22cd3d8e55781aee4b01aac72b4ec60ef1d8cf authored over 3 years ago by Daniel Bryce <[email protected]>
Merge pull request #52 from rpgoldman/container-spec

2ed01e655d27f2da88d0ca56a4da9b0d4a007b63 authored over 3 years ago by rpgoldman <[email protected]>
Update LUDOX test rubric.

e78cc5130d1fa81ba53dc7a11ca6167af8ae22d5 authored over 3 years ago by Robert P. Goldman <[email protected]>
Use paml:ContainerSpec instead of string.

Add a ContainerSpec Identified object that pairs a string with a prefix map, suitable for use wi...

2281134458c88ad6d1a77112a572080f1498e98d authored over 3 years ago by Robert P. Goldman <[email protected]>
Add definition of PAML ContainerSpec class.

bf2faa9a89445b810fc004a0fe3e7edad8b5257a authored over 3 years ago by Robert P. Goldman <[email protected]>
Merge pull request #51 from rpgoldman/add-container-spec

2104a1d5a4aa1bab1c9f8197d513ed5cf3554fa7 authored over 3 years ago by rpgoldman <[email protected]>
Fix test whitespace.

5ee8f8162d4697cd5133b805389f1ddf63a0e135 authored over 3 years ago by Robert P. Goldman <[email protected]>