github.com/Bioprotocols/labop commits | Ecosyste.ms: OpenCollective

Merge pull request #25 from SD2E/sbol-uml

SBOL UML first implementation

dbe533da0145d1586c74c3303c2f9a66147f7130 authored over 3 years ago by Jacob Beal <[email protected]>

Add UML model as standard turtle.

`uml-flattened.ttl` is the Turtle version of `uml.ttl`, which seems to
be Turtle*.

6d9300f883279d17205b775deca09ea6dcd51899 authored over 3 years ago by Robert P. Goldman <[email protected]>

Improve documentation

Adds a sentence about what PAML is to the README.
Adds references to the defining UML section fo...

7de0c9668951c557983fc79260812f765bb7f6b9 authored over 3 years ago by Jake Beal <[email protected]>

Address #13 through implicit injection of ForkNodes

When an ObjectFlow is added using the Activity.use_value helper function, the code now automatic...

6a72159ac9d423792864ae67ad8754f7aeeb901a authored over 3 years ago by Jake Beal <[email protected]>

Implement validation check for nondeterministic multi-outputs per discussion on #13

This commit adds a validator for uml.Activity objects that checks to see whether any of the Acti...

b1b16d39878587d780376fb7c625fe949c24a516 authored over 3 years ago by Jake Beal <[email protected]>

include library tweak

283c676d6f87e31ee453d976bf519df25ea65fab authored over 3 years ago by Jake Beal <[email protected]>

fix more case bugs, stabilize ordering of action builds; clean out some obsolete material

dd81685909323bc408fe8957c9a9e1c3e7aeff74 authored over 3 years ago by Jake Beal <[email protected]>

nearly there on protocol smoke-test

639005c5f6741817ab31c4c9567563162598180b authored over 3 years ago by Jake Beal <[email protected]>

get utils test running by temporarily disabling some non-yet-converted materials

b98a49d5f18aa7f07e06ae22be76b3461aac0189 authored over 3 years ago by Jake Beal <[email protected]>

another build typo

ca982212fd19e9dcb0b91bb816baf0716b51a1e4 authored over 3 years ago by Jake Beal <[email protected]>

Add uml package to setup.py

4ada3b90bc2f042c9eda42c71c6343267f76028a authored over 3 years ago by Jake Beal <[email protected]>

successful test of library building with UML classes

24c4d35efb9d077c19bec6c9e50f9901eedf182c authored over 3 years ago by Jake Beal <[email protected]>

working up to UML-based smoke test

3b3605428d9e9cf8881c74756e2784d2d7524d17 authored over 3 years ago by Jake Beal <[email protected]>

working on implementation of first UML test

4d217200e30b4eab7a9345dc13b0c38e4ff70748 authored over 3 years ago by Jake Beal <[email protected]>

Merge branch 'samplearray' into sbol-uml

# Conflicts:
# paml/paml.ttl

9c6306835668899eb137c3b51236e9248e7be5f0 authored over 3 years ago by Jake Beal <[email protected]>

rebuild other two libraries as well

1accc74a5ae69660ae7138f05e288c6168c79a36 authored over 3 years ago by Jake Beal <[email protected]>

working on UML implementation

87b121067f255eb4b5a41c2ae776a0595a687a82 authored over 3 years ago by Jake Beal <[email protected]>

move uml ttl to its own package, ensure that it can load

6ddb92c80c8b456624209f46c7ae556953c1b04f authored over 3 years ago by Jake Beal <[email protected]>

Add value specifications and constraints

d0efcfe0279349af73225ceeaa1f082e8ced7b02 authored over 3 years ago by Jake Beal <[email protected]>

added properties; need to add two more classes

ddb7f4c9ac7b9d3c97dac172839b330432d6207f authored over 3 years ago by Jake Beal <[email protected]>

Add pins and behavior invocations, define PAML Protocol as a uml:Activity, Primitive as a uml:Behavior.

9d0d739b5381228314957af2e7eceaf2d8b6da47 authored over 3 years ago by Jake Beal <[email protected]>

First draft of UML classes, though still missing all properties

30ec6efef39fab0152d2a60a36ad0e3d20d65e7b authored over 3 years ago by Jake Beal <[email protected]>

Filling in properties on containers and data

8434467e882ae532e866aed858175fb92a1e98b0 authored over 3 years ago by Jake Beal <[email protected]>

also remove properties

b7f5920d06f5d992b654bdb6b5d85e10595aff6d authored over 3 years ago by Jake Beal <[email protected]>

working on a new approach to samples

0c4dffc0b81c7d11c2261bd0c859b2311f7a0974 authored over 3 years ago by Jake Beal <[email protected]>

upgrade sbol3, sbol-factory, correct incorrect link in growth protocol

66a90a36c7056ca7fec59da2a82751dd841bbb7a authored over 3 years ago by Jake Beal <[email protected]>

update library mappings file to match current state of libraries

c98c94ec1ea8ec020570f24451a658bf0c4e843a authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #10 from SD2E/growth-protocol

Growth protocol

f8e2f207520ab9348512f21234203ade4e5cc9b8 authored over 3 years ago by Jacob Beal <[email protected]>

Complete growth curve protocol

6a432515b57525dfd962f296893ce2039dbc9000 authored over 3 years ago by Jake Beal <[email protected]>

First successful end-to-end generation of markdown for growth protocol

f684f8cccf993de1c4682421367e28ecfdb55c7a authored over 3 years ago by Jake Beal <[email protected]>

making progress toward resolving growth curve

0392a053290a89e67fee0b41a72de433a9fef385 authored over 3 years ago by Jake Beal <[email protected]>

debugging markdown conversion of growth protocol

f98d2a5129c3b2006624bc38a7d80385fcecaff3 authored over 3 years ago by Jake Beal <[email protected]>

generalize conversion to handle multi-protocol documents

e11a69c9fbcf56485f99d0d2a4c517257e3bf4ae authored over 3 years ago by Jake Beal <[email protected]>

add markdown expansion for most primitives, fix broken test

e15ab1400a4d626fa09b8168522eb57330abcb21 authored over 3 years ago by Jake Beal <[email protected]>

automatic merging of ranges

0ba4d153d803a7780b728513b9a8509892067b3e authored over 3 years ago by Jake Beal <[email protected]>

continued cleanup of markdown conversion

b96833622580bcef6a6b43b9a0c149fbd31bb181 authored over 3 years ago by Jake Beal <[email protected]>

generalizing markdown conversion

fba5a5998477d51f3bd25bae71617cddb424eb8a authored over 3 years ago by Jake Beal <[email protected]>

fix failing tests

0aadc01e432a2cc45f65c9bc20118bf6af308769 authored over 3 years ago by Jake Beal <[email protected]>

inference using LocatedData; draft of subprotocol type inference

7ef183f319db105d9d9b8f4de0e694410ecf25fc authored over 3 years ago by Jake Beal <[email protected]>

library inference fully prototype

f6c92dce11ffa23213e939bb7307d8ad31b2dea4 authored over 3 years ago by Jake Beal <[email protected]>

add numpy to dependencies

d30c16d5dc0470f959e9aba420c40dd0f3241f29 authored over 3 years ago by Jake Beal <[email protected]>

continued work on growth protocol

6df39f234090f51dd14359ca144e6e38cdd29693 authored over 3 years ago by Jake Beal <[email protected]>

Better approach to coordinate reduction

2ac1a587442db36aecf2828507e6508c5cfa57e0 authored over 3 years ago by Jake Beal <[email protected]>

working on container inferencing

ca8e5787f7663404bdccc5c0c97047661d547c7d authored over 3 years ago by Jake Beal <[email protected]>

Merge commit '8e5f1a5b9d3d71ad1763e646bbde6734631f962e' into growth-protocol

7e024644e1cec82b1fc3b38d7112131bcff71830 authored over 3 years ago by Jake Beal <[email protected]>

fix package install

19f6f7dab604ce172ec5446ee51302fceb3902c3 authored over 3 years ago by Jake Beal <[email protected]>

cleaning up type inference

20da98a837fe1c5c0f868708c739026f478fbd21 authored over 3 years ago by Jake Beal <[email protected]>

Update script for rendering growth curve protocol

8e5f1a5b9d3d71ad1763e646bbde6734631f962e authored over 3 years ago by Bryan Bartley <[email protected]>

continued work on type inference

faadeb87676751a0f686fc640ed5c7cd39c70192 authored over 3 years ago by Jake Beal <[email protected]>

working on type inference

3c18ea36159bb4228f9d073410676171de38523e authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #9 from SD2E/growth-protocol

Growth protocol complete draft

840c81cddc3fb930aec06f35e42f4516a141202e authored over 3 years ago by Jacob Beal <[email protected]>

complete draft of growth curve protocol

20348fa7c601db9b0c5f22cddd2b5a5439340181 authored over 3 years ago by Jake Beal <[email protected]>

subprotocol for growth curve is building fully

332b91337fd1326ffa48dd423e85ff44b942bf56 authored over 3 years ago by Jake Beal <[email protected]>

subprotocol inputs and outputs

90359dab5cca785033f1ca0a6f46df1d548a0379 authored over 3 years ago by Jake Beal <[email protected]>

macro functions for adding inputs and outputs

f598f929fb15b1b252296e1d7df6d76b6b62efce authored over 3 years ago by Jake Beal <[email protected]>

Remove doc requirement from pin calls, implicit flows through use of activities in input slots

e02bd13804ac9ac85e60a38d855a3d0e96c3e349 authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #8 from SD2E/lazy-libraries

only libraries actually used are imported

f275be70529eb6ad00debe217b33468e2bccbbd4 authored over 3 years ago by Jacob Beal <[email protected]>

only libraries actually used are imported

1d7b7221df4a03d1befee38a08dae9e88ac93103 authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #7 from SD2E/markdown-package

Markdown package

51bf99857158a92a199fc44bf5459c2ead89dd77 authored over 3 years ago by Jacob Beal <[email protected]>

use python 3.9, not 3.8

ff599690a5297953eec3fc011176460d5ce2ac67 authored over 3 years ago by Jacob Beal <[email protected]>

add missing dependency

0f4fba9bc2b8e4c990ba9a9763e3d6b5812f3dec authored over 3 years ago by Jake Beal <[email protected]>

a bit more cleanup

1a59952dc26a756456344625cafe555bdcbe5aa4 authored over 3 years ago by Jake Beal <[email protected]>

Update python-package.yml

d4e4a7caea168d00a69e9ee32c7731318cadb8b3 authored over 3 years ago by Jacob Beal <[email protected]>

markdown package initial split and test

41643cc9e9dfae62250bf08b58b40b86e3958848 authored over 3 years ago by Jake Beal <[email protected]>

continuing to work on markdown; also fixing python property names

10f7f24a9d2c0c7326e1e9545bb02900c26e7b56 authored over 3 years ago by Jake Beal <[email protected]>

starting to split protocol-to-markdown script into package tests

27365afd460984fb5a100f0244bf9e375c9e0f1d authored over 3 years ago by Jake Beal <[email protected]>

diff-based testing; may have stability issues, may also need to be changed to n-triples

10571bf4b6b8297c6a9c61fa15bd41f011c327c0 authored over 3 years ago by Jake Beal <[email protected]>

set up library rebuild to operate correctly when run from base directory

6af906b826731fcde8df648aa364bb2787c3bb4c authored over 3 years ago by Jake Beal <[email protected]>

Merge commit 'e354d3b9d795a9ff6d7721e8208ef25e265d65cb' into main

da19f7e4b894e3ae04a49a7aa605999da9e3f813 authored over 3 years ago by Jake Beal <[email protected]>

working on getting pytest working for PAML

8ae57677377dd384bd9dbb1b898584945dcaaa6d authored over 3 years ago by Jake Beal <[email protected]>

Update python-package.yml

e354d3b9d795a9ff6d7721e8208ef25e265d65cb authored over 3 years ago by Jacob Beal <[email protected]>

remove linting

sbol_factory classes are guaranteed to fail lint, so remove from the test workflow

565f8b102cfa6a7c3c31b6d3e5fb0d0703e3e1dc authored over 3 years ago by Jacob Beal <[email protected]>

Create python-package.yml

c9cc742c5b5d1b8820b5e4e9af945efa1fa845bd authored over 3 years ago by Jacob Beal <[email protected]>

working on adding tests

59c1a8bf48af369ca921be80278596302b021f5e authored over 3 years ago by Jake Beal <[email protected]>

making progress on growth protocol; shifting library from locations to located samples

0e53ee7b7deb64138157b22b8cb4107d0f728585 authored over 3 years ago by Jake Beal <[email protected]>

Merge pull request #6 from SD2E/factor_out_helper_functions

Factor out helper functions

75e5fc10aea66d3194c53bcd06300aef2d4fc802 authored over 3 years ago by Jacob Beal <[email protected]>

Merge branch 'factor_out_helper_functions' of https://github.com/SD2E/paml into factor_out_helper_functions

# Conflicts:
# paml/__init__.py
# paml/paml.ttl

75e75349092c48a7c5f2b8303307b7c2056c0728 authored over 3 years ago by Jake Beal <[email protected]>

end-to-end run using library operators

728642f1a8622c007f3e3a39c8d980a97cba7644 authored over 3 years ago by Jake Beal <[email protected]>

Merge branch 'factor_out_helper_functions' of https://github.com/sd2e/paml into factor_out_helper_functions

14213eacf2f09d4a03fc3817bf52474cb249b499 authored almost 4 years ago by Bryan Bartley <[email protected]>

Update README

72c4abd064dd5f85bcf29f748ce99e23d8be2f6a authored almost 4 years ago by Bryan Bartley <[email protected]>

Use graphviz clusters to organize object compositions

2a8549b5364e4861726b193b10a0a9ab89aaa9b8 authored almost 4 years ago by Bryan Bartley <[email protected]>

Merge branch '4-fix_datatype_properties' into factor_out_helper_functions

0395b1cb625e9be1ca1e8ef549a7c7265bbf615c authored almost 4 years ago by Bryan Bartley <[email protected]>

Fix #4

d2ecb43ce374204fc3afd8ba79df7b99d4e90581 authored almost 4 years ago by Bryan Bartley <[email protected]>

Add script for visualizing Document tree

101f3be15854e0e70a4d9ede0f819415bd65c080 authored almost 4 years ago by Bryan Bartley <[email protected]>

working on libraries

6d809c78c79c97634b715e96ea0b2f07009aa674 authored almost 4 years ago by Jake Beal <[email protected]>

working on library-based protocol building

b102daa623ef0474c90e08f41f582cd871903b46 authored almost 4 years ago by Jake Beal <[email protected]>

add libraries for growth protocol

3ffb59f4be76438cc74f0efca55ba985ea13fb7c authored almost 4 years ago by Jake Beal <[email protected]>

Merge branch 'main' into factor_out_helper_functions

48ef3af81c1c3e30a85ffbe316666ea663f686fe authored almost 4 years ago by Jake Beal <[email protected]>

working on library-building

d85d8ea3dc4afcac5a0f84cbb65d79ead2452984 authored almost 4 years ago by Jake Beal <[email protected]>

Add helper functions for instantiating PrimitiveExecutables

37ea70098301aabc02f3e239259ac18d0eb8930f authored almost 4 years ago by Bryan Bartley <[email protected]>

library-building in progress

1a26d6c8362f50e778b125e49af3e1980328fe32 authored almost 4 years ago by Jake Beal <[email protected]>

fix to work with current sbol-factory release

dcec60c62928f300ee5118f6a648b30dcb1632b1 authored almost 4 years ago by Jake Beal <[email protected]>

moving smoke-test examples into a test directory, refactoring to match sbol factory

51ff94d237a9e86c17e5f1db97e5e694d6cc938b authored almost 4 years ago by Jake Beal <[email protected]>

Merge pull request #3 from SD2E/remove_git_sumbodule

Configure pip module

3cbe803adc1d48d055e03d53a0fb0a3797a203b0 authored almost 4 years ago by Jacob Beal <[email protected]>

Configure module

8e25d866a73a7b98ed52040a596fdc38520bd28e authored almost 4 years ago by Bryan Bartley <[email protected]>

comment out some classes that look like they will not be useful

6b9a4ab1d7ea4413c8d073996734d967057a9b39 authored almost 4 years ago by Jake Beal <[email protected]>

end to end complete test

91cf4a14ee57b64b438379ea30e4d27dd964dc4f authored almost 4 years ago by Jake Beal <[email protected]>

Fix fencepost error on step number in Excel

db162d2a8bbede08794c94f71e62d2e753bc67f7 authored almost 4 years ago by Jake Beal <[email protected]>

first full output including datasheet

11d494cd1096dcae4c173b00d402c40df9d397ec authored almost 4 years ago by Jake Beal <[email protected]>

first end-to-end pass on a protocol

20187ddc22697725dcea597bcf1cea1d5f2f365b authored almost 4 years ago by Jake Beal <[email protected]>