Bioprotocols Working Group commits | Ecosyste.ms: OpenCollective

Example for Mike Fero

github.com/Bioprotocols/laboped - e8a182979345803b59c7b68b93353f2b633916fd authored almost 3 years ago by Daniel Bryce <[email protected]>

Fix some grammatical snafus

github.com/Bioprotocols/labop - ad55db90ac860c1aa8078a587f585608aa784adc authored almost 3 years ago by bbartley <[email protected]>

Add Markdown converter example

github.com/Bioprotocols/labop - 6bd12562385db14dd25ea6cbbe09d022fb853f10 authored almost 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #16 from Bioprotocols/disclaimer

added disclaimer modal

github.com/Bioprotocols/laboped - 57a67fec3395c9289086f96ef8bc5c58368f375b authored almost 3 years ago by Daniel Bryce <[email protected]>

added disclaimer modal

github.com/Bioprotocols/laboped - fab47583c3a4aded134fd650f070defc5144a698 authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #15 from Bioprotocols/ui-adjust

minor ui adjustments

github.com/Bioprotocols/laboped - 934be523feb308c5cb7449b8f399557c30a5f194 authored almost 3 years ago by Daniel Bryce <[email protected]>

minor ui adjustments

github.com/Bioprotocols/laboped - fe18551b20d6a0bd667bd28f6c3344d4168a848f authored almost 3 years ago by Daniel Bryce <[email protected]>

Title image with icon from Noun Project (#14)

When I was migrating this repo from my personal GitHub account to Bioprotocols, I was prompted t...

github.com/Bioprotocols/container-ontology - 9869793e2566714c2c75ff6e2eae22f4d05a7d77 authored almost 3 years ago by rpgoldman <[email protected]>

Merge pull request #14 from Bioprotocols/output-serialize

Output serialize

github.com/Bioprotocols/laboped - dafc42a8f9e3b5a0beafb9c5f836c75ea1b83986 authored almost 3 years ago by Daniel Bryce <[email protected]>

Converting protocols, subprotocols, and protocol-primatives

github.com/Bioprotocols/laboped - fcf20d4f1b43aa5d739921b4f48ed5cf6ecd62ea authored almost 3 years ago by Daniel Bryce <[email protected]>

Fixed serialization for outputs

github.com/Bioprotocols/laboped - 465e5c4f5fde2469f95a2e4a0a5ac976380682a5 authored almost 3 years ago by Daniel Bryce <[email protected]>

make App.css more specific

github.com/Bioprotocols/laboped - 23ecab79551dddce67ed33ef1c3a973d9ef49b67 authored almost 3 years ago by Jack Ladwig <[email protected]>

Merge pull request #12 from Bioprotocols/gui-adjust

Gui adjust

github.com/Bioprotocols/laboped - 15c2af781695ff58c6c36cd488cda83b021ea3a1 authored almost 3 years ago by Daniel Bryce <[email protected]>

fix context menu size

github.com/Bioprotocols/laboped - cb56966c51d4380423287234e91b26592abb2337 authored almost 3 years ago by Daniel Bryce <[email protected]>

added user guide

github.com/Bioprotocols/laboped - 1976c302a4f02fcfe3bddefc82130bd328852c8a authored almost 3 years ago by Daniel Bryce <[email protected]>

ref from readme

github.com/Bioprotocols/laboped - 8c106c90da3ba742b3ce4d0dd24f2966315fb9af authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #10 from Bioprotocols/readme-update

Readme update and code cleanup

github.com/Bioprotocols/laboped - b41dfe9ee8340ad789b8d4c555683b7cd2d75f5b authored almost 3 years ago by jgladwig <[email protected]>

updates to Pipfile and add Pipfile.lock

github.com/Bioprotocols/laboped - 9453f276a9d90e2e02db85e942cfa0490059a6cf authored almost 3 years ago by Jack Ladwig <[email protected]>

Update README.md

fix typo referencing backend/ when it should have been frontend/web/

github.com/Bioprotocols/laboped - ac7153a04a72e99f99a2725c37a854eb67152c85 authored almost 3 years ago by jgladwig <[email protected]>

readme-update

github.com/Bioprotocols/laboped - 16723d3d53b2095fe5afa7614d631447c09964d7 authored almost 3 years ago by Daniel Bryce <[email protected]>

ludox protocol

github.com/Bioprotocols/laboped - e8a9769a845f43992c933d2622d7d76e28e92c73 authored almost 3 years ago by Daniel Bryce <[email protected]>

readme instructions

github.com/Bioprotocols/laboped - d92c5fc3b333fcc16f852d4494a71a73477cbe15 authored almost 3 years ago by Daniel Bryce <[email protected]>

cleanup errors in console

github.com/Bioprotocols/laboped - fae4ecb16b9eb7848b125c648254c80bc6fb71a4 authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #9 from Bioprotocols/io-types

Support for inputs, outputs, and parameters.

@jgladwig I'm merging this because its part of a...

github.com/Bioprotocols/laboped - e4d00e23e712ea9f59e2ca54a2e5213c25b9d897 authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #103 from Bioprotocols/nb-tests

Nb tests

github.com/Bioprotocols/labop - daafdeb328d45f36d7fd2abbfc2aca8b4b6fc9a9 authored almost 3 years ago by Daniel Bryce <[email protected]>

fix issues with save io types

github.com/Bioprotocols/laboped - 2737412a65e0279342f949e2601ae046d7506fad authored almost 3 years ago by Daniel Bryce <[email protected]>

skip test with nondeterminsm in nt file output

github.com/Bioprotocols/labop - 2871f94b733ff786fbc17e54e11de11654673424 authored almost 3 years ago by Daniel Bryce <[email protected]>

updated rubric

github.com/Bioprotocols/labop - f4e9b0d959a60539bf670ac8a295372ac0e5b6b6 authored almost 3 years ago by Daniel Bryce <[email protected]>

address Jake's review

github.com/Bioprotocols/labop - 71bca2c47499a140673fe3d18e43667c52d8a5ff authored almost 3 years ago by Daniel Bryce <[email protected]>

Basic Version of Canned types.

github.com/Bioprotocols/laboped - ca67449aa8b86556f11ee64f20dcdc2791955a84 authored almost 3 years ago by Daniel Bryce <[email protected]>

ui logic and parameter components

github.com/Bioprotocols/laboped - 965ac48da27c2a07882f46439c48893f415ae93e authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #108 from Bioprotocols/fix-execution-tokens

Fixed bug in token generation for outputs that chose additional proto…

github.com/Bioprotocols/labop - 76b58606c81441a69dedc75e556a85cc0a8d124b authored almost 3 years ago by Daniel Bryce <[email protected]>

Fixed bug in token generation for outputs that chose additional protocol edges.

github.com/Bioprotocols/labop - fabaf44aa9c160d75bbb0ec29474006744ab0e72 authored almost 3 years ago by Daniel Bryce <[email protected]>

allow loading rete graph files from local filesystem

github.com/Bioprotocols/laboped - 9d5b5683b5a84b49f31b49d14a357454ca061572 authored almost 3 years ago by Jack Ladwig <[email protected]>

Merge pull request #105 from Bioprotocols/activity-primitive-disjoint-fresh

Add disjoint relationship

github.com/Bioprotocols/labop - d88c3b4d06a7c8f8cdb295a08b81f94bc503eda0 authored almost 3 years ago by bbartley <[email protected]>

Merge pull request #63 from Bioprotocols/docs-refactor

WIP: Docs refactor

github.com/Bioprotocols/labop - 168eb725d9b635eacf1369a3a376c9b40ede1627 authored almost 3 years ago by bbartley <[email protected]>

Merge branch 'main' into docs-refactor

github.com/Bioprotocols/labop - e4f899a764db664ecf4ee110c12c71c397632700 authored almost 3 years ago by Bryan Bartley <[email protected]>

save current protocol when making a new protocol

there is more that can be considered here but at least
avoid losing state when making a new prot...

github.com/Bioprotocols/laboped - 6c57a42803a2acbeee1f9faf9185e76378ac83fa authored almost 3 years ago by Jack Ladwig <[email protected]>

add rebuilding primitives modal

github.com/Bioprotocols/laboped - 9891a785f19381c34eec97ac60a39502be4a94c1 authored almost 3 years ago by Jack Ladwig <[email protected]>

Add disjoint relationship

github.com/Bioprotocols/labop - 70b68e6ba9fc4417d35f2dece0e65b93f04e6007 authored almost 3 years ago by Bryan Bartley <[email protected]>

misc bug fixes and improvements:

- move download to a lazy rdf generation on request
- fix(?) race condition in component loading...

github.com/Bioprotocols/laboped - f834e70c98a0b3e56c1a04dcf058e9dc0b31a897 authored almost 3 years ago by Jack Ladwig <[email protected]>

call saveProtocol with name and not object

github.com/Bioprotocols/laboped - 74ac36a55e6e6273717e873de337308251929a3b authored almost 3 years ago by Jack Ladwig <[email protected]>

consolidated menu per protocol

github.com/Bioprotocols/laboped - 6af210b4c17a343f234bd27beda16a1a23bd65ce authored almost 3 years ago by Daniel Bryce <[email protected]>

Remove obsolete Makefile rule.

github.com/Bioprotocols/container-ontology - a9276d29e07bfc3ca7899b9fbbe6b1d715f33bf1 authored almost 3 years ago by Robert P. Goldman <[email protected]>

fix duplicate generation of primitives

github.com/Bioprotocols/laboped - ba107dc5d22e2e351e22695eb52cb520e35655fd authored almost 3 years ago by Daniel Bryce <[email protected]>

saving names for input and output

github.com/Bioprotocols/laboped - 49bfcf84e7ce6cbe6f26a738ff91bb2748cae3b9 authored almost 3 years ago by Daniel Bryce <[email protected]>

checkpoint for fixing primitives

github.com/Bioprotocols/laboped - b302bb1f824cafde4a332fec74646d9dd2cba27f authored almost 3 years ago by Daniel Bryce <[email protected]>

wrap up saving/deleting/renaming

also attempt to reopen the previous protocol on reload

github.com/Bioprotocols/laboped - ba81fc35e3eb151d6ef97da85c76be2727606b7a authored almost 3 years ago by Jack Ladwig <[email protected]>

remove paml_check dep from demo

github.com/Bioprotocols/labop - 0dbe6c3b821041d08eb81704cbce17a39bf6bdb5 authored almost 3 years ago by Daniel Bryce <[email protected]>

conditionally run container_api if import succeeds

github.com/Bioprotocols/labop - 79c99b16f47948eb7c2d341f8dcefa1ea40f5e78 authored almost 3 years ago by Daniel Bryce <[email protected]>

enable nbtest and pre-commit

github.com/Bioprotocols/labop - 7f35107df105400a9291aa759c756a3f17408ba6 authored almost 3 years ago by Daniel Bryce <[email protected]>

Remove old m4 file.

github.com/Bioprotocols/container-ontology - c1ba40508eb292b34510e999a0a21b03718e8a00 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Update owlery catalog of ontologies.

Use .omn (OWL Manchester notation) in place of Turtle file.

github.com/Bioprotocols/container-ontology - 50290a1fa05a6e2cc5ad9ab371caf4472eb9aa25 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Merge pull request #70 from Bioprotocols/installation-readme

Correct the installation information in README.txt

github.com/Bioprotocols/labop - 590ef15bfe25b29bac509765e6c41c20cf320db6 authored almost 3 years ago by bbartley <[email protected]>

Improved and simplified Owlery service configuration.

github.com/Bioprotocols/container-ontology - 4cbf815dd9fbe43f2500642292dd387a13c2b324 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Improved the documentation.

github.com/Bioprotocols/container-ontology - ec9c0d08a8091b8339f8c3ba3dbc77474fccc9dd authored almost 3 years ago by Robert P. Goldman <[email protected]>

Merge branch 'main' into installation-readme

github.com/Bioprotocols/labop - f6983bea353557c0a722a024d37d6a803c63f849 authored almost 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #68 from rpgoldman/fix-restrictions

Fix the malformed OWL restrictions.

github.com/Bioprotocols/labop - 81c3ade34837cd39339dc290ed6bdaad1438e228 authored almost 3 years ago by bbartley <[email protected]>

Merge pull request #100 from Bioprotocols/backward_compatibility

Backward compatibility

github.com/Bioprotocols/labop - 2d6daaa50850e4d309f69a65a73f534b08d0037a authored almost 3 years ago by bbartley <[email protected]>

Set minimum Python version to 3.7

github.com/Bioprotocols/labop - fb980e2ec13b349d8b40c5107ffed591cda1c2c3 authored almost 3 years ago by Bryan Bartley <[email protected]>

Update workflow

github.com/Bioprotocols/labop - f2aee721b57462a2b530406d780dc2163d08a3b4 authored almost 3 years ago by Bryan Bartley <[email protected]>

Unpin sbol3 version

github.com/Bioprotocols/labop - f220b148092f37fed12ad3d2201054f77456e5e7 authored almost 3 years ago by Bryan Bartley <[email protected]>

initial pass add adding per protocol dropdown items for:

- open
- save
- name
- delete

github.com/Bioprotocols/laboped - 79c448360415910f9e744bd36278a14dcaafd9b8 authored almost 3 years ago by Jack Ladwig <[email protected]>

Fix directlyComprises predicate

github.com/Bioprotocols/labop - 4060791228c2217795551252a19a6de753cd6719 authored almost 3 years ago by Bryan Bartley <[email protected]>

Remove obsolete notebooks

These notebooks (and the ancillary data) were there to help develop the code that is now in owl_...

github.com/Bioprotocols/labop - 4c24a410f91dec73af56fdbff1a6aeeff87d8d17 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Test fix.

github.com/Bioprotocols/labop - 521794d4649f30eec4b921146e87647293ac5b56 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Add crude RDF diff script.

github.com/Bioprotocols/labop - e2dbdba85a38ee6359ddefbeda23a28aefee0efd authored almost 3 years ago by Robert P. Goldman <[email protected]>

Fix restrictions tests.

github.com/Bioprotocols/labop - a7ed38e2b9b402a3e052c65e1b620fe79455939b authored almost 3 years ago by Robert P. Goldman <[email protected]>

fixed broken status.

github.com/Bioprotocols/laboped - 0f606ea9162de0cb3ed5dbb3fdbdd319a6aed2ec authored almost 3 years ago by Daniel Bryce <[email protected]>

Add owl_rdf_utils to the list of packages to install.

Also:

1. Reformat with black
2. Remove unused imports

3. owl_rdf_utils is not a dependency.

github.com/Bioprotocols/labop - f1e278fb699c1ecba048fcb6aa39f6c16c6760d2 authored almost 3 years ago by Robert P. Goldman <[email protected]>

Multiple script fixes.

Minor bugs here and there and some clarifying docs

github.com/Bioprotocols/labop - 4d44ab3edc48b11f947e24c4370628e5c131e07f authored almost 3 years ago by Robert P. Goldman <[email protected]>

broken state for sharing

github.com/Bioprotocols/laboped - 75efb787ff5284122f8e05c27e6971215db9f310 authored almost 3 years ago by Daniel Bryce <[email protected]>

Update dependencies

github.com/Bioprotocols/labop - 02a26956bcd80b0c3d6b35d3b6fa20476f67562f authored almost 3 years ago by Bryan Bartley <[email protected]>

Merge branch 'main' into fix-restrictions

github.com/Bioprotocols/labop - 02fc89b1649da4d8123e535801952d455f817f6f authored almost 3 years ago by Bryan Bartley <[email protected]>

Add test to validate Restriction syntax for paml and uml

github.com/Bioprotocols/labop - 23a04c04baa9a206e2863addaadeed48b80f5516 authored almost 3 years ago by Bryan Bartley <[email protected]>

Clean up Restrictions in ontology files

github.com/Bioprotocols/labop - 69c36897682e01404fde26dba49ce329df366614 authored almost 3 years ago by Bryan Bartley <[email protected]>

Updating protocols with i/o in pallete

github.com/Bioprotocols/laboped - 53ce20b4229636d27cc0afc85d75897237925598 authored almost 3 years ago by Daniel Bryce <[email protected]>

ignores

github.com/Bioprotocols/laboped - 19f13f2c9997dafb0c29b2efca9964985f1f403a authored almost 3 years ago by Daniel Bryce <[email protected]>

Several cleanups to properly store and retreive protocols.

github.com/Bioprotocols/laboped - 42ae2731146e0f314d21c25d9ba6b8761337efac authored almost 3 years ago by Daniel Bryce <[email protected]>

initial cleanup of reqs and update readme

github.com/Bioprotocols/laboped - 2c25f42a1003d9be9ef276b7e83633d8f2be5509 authored almost 3 years ago by Jack Ladwig <[email protected]>

Update README.md

github.com/Bioprotocols/labop - 4a2bebd24d57baf227a58898bf24e52751ee1e1f authored almost 3 years ago by bbartley <[email protected]>

Merge pull request #94 from Bioprotocols/66-package

66 package

github.com/Bioprotocols/labop - 53347ff09de8745514bfadaa6714cb8e4cbd2a28 authored almost 3 years ago by bbartley <[email protected]>

Disable jupyter notebook tests

github.com/Bioprotocols/labop - a3277764de8bbe496333e589748fc537e01c5992 authored almost 3 years ago by Bryan Bartley <[email protected]>

Disable tests

github.com/Bioprotocols/labop - 2db2d1509e0bb0bbbbf4f387ef18e20859073f74 authored almost 3 years ago by Bryan Bartley <[email protected]>

Disable container_api

github.com/Bioprotocols/labop - bc234f27136b849c013df49d5a611ce5a95d3068 authored almost 3 years ago by Bryan Bartley <[email protected]>

That's not working--remove container-ontology

github.com/Bioprotocols/labop - 1cbb1e7334f181ae5ade37f7393237f1a17f5f48 authored almost 3 years ago by Bryan Bartley <[email protected]>

Add wrapper for setup script that installs git submodules

github.com/Bioprotocols/labop - d00ec2f611cb2d100500264ab735b63a898f0cb2 authored almost 3 years ago by Bryan Bartley <[email protected]>

Add container ontology as git submodule

github.com/Bioprotocols/labop - 59569801701cf804b4abad51f3af00459e3c8db5 authored almost 3 years ago by Bryan Bartley <[email protected]>

Remove paml-check from extras

github.com/Bioprotocols/labop - 68c7f62873d853d8e460c26ec39cfca12072e9ab authored almost 3 years ago by Bryan Bartley <[email protected]>

Move paml-check to git submodule

github.com/Bioprotocols/labop - 4b93f650050deffa8b8c3ad71554c60b9c39026a authored almost 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #90 from Bioprotocols/71-license

Add license

github.com/Bioprotocols/labop - dea4b554b0b9ae1c1aaf15f676fce28e3d078370 authored almost 3 years ago by bbartley <[email protected]>

Change package name to pypaml

github.com/Bioprotocols/labop - faa166dc63480cd94ce850a45a006f2afeed98eb authored almost 3 years ago by Bryan Bartley <[email protected]>

Add license

github.com/Bioprotocols/labop - 2649772cd409e6b31c8b54f852a5d24d5af4378b authored almost 3 years ago by Bryan Bartley <[email protected]>

Merge pull request #8 from Bioprotocols/rdf-roundtrip

Rdf roundtrip

github.com/Bioprotocols/laboped - 39ca4a9729ba4e56992bf3ee0dfe44681b2a86fd authored almost 3 years ago by Daniel Bryce <[email protected]>

Added Timepoint ports and working on Input components.

github.com/Bioprotocols/laboped - 23ddbacfbd76df8b5f828c9a20b4fe0dd1162728 authored almost 3 years ago by Daniel Bryce <[email protected]>

Setup place to add conversion to opentrons. Based on Autoprotocol conversion by removing specifics.

github.com/Bioprotocols/labop - 09b5b9037571cd38838b1d224b14a57f3940663d authored almost 3 years ago by Daniel Bryce <[email protected]>

Merge pull request #88 from Bioprotocols/58-clean_out_opil

Remove references to opil

github.com/Bioprotocols/labop - 8a49978ec03f0ec78bcaf9592ebe88e64a5d1271 authored almost 3 years ago by bbartley <[email protected]>

Remove references to opil

github.com/Bioprotocols/labop - cea48a31edd7e8066c8e3a5ba7cf8a69aaf149f0 authored almost 3 years ago by Bryan Bartley <[email protected]>

Add instructions for installing paml-check

github.com/Bioprotocols/labop - 4e76529f2a2c3e44d9c01955f2a8d6c1ef880d20 authored almost 3 years ago by bbartley <[email protected]>

Merge pull request #79 from Bioprotocols/78-upgrade_rdflib

Upgrade rdflib dependency

github.com/Bioprotocols/labop - 1c0548e7cae8f36a066eecb5baad336b4751fd5a authored almost 3 years ago by bbartley <[email protected]>