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chore: updates to enable processes #10

Merged
merged 55 commits into from
May 7, 2024
Merged

chore: updates to enable processes #10

merged 55 commits into from
May 7, 2024

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AlexPatrie
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@AlexPatrie AlexPatrie commented Apr 28, 2024 •
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What does this PR do?:

  • Fixes an issue with process result retrieval from composite emitter.
  • Performs "housekeeping" on existing TelluriumProcess and CopasiProcess process_bigraph.Process implementations.
  • Adds AmiciProcess to biosimulator_processes/processes library.
  • Creates and adds ODEComparator processes to processes library for simulator comparison.
  • Adds ./compare_api library which contains the spec and logic for the Compare REST API.

AlexPatrie added 30 commits April 26, 2024 18:43
@AlexPatrie
updates
e6bb954
@AlexPatrie
feat: updates to synthesizer process
f637a9b
@AlexPatrie
chore: removed unused and refactored for env
3cd8ff9
@AlexPatrie
chore: update savepoint
8f9e53b
@AlexPatrie
fix: added update to simulation output
3be8523
@AlexPatrie
fix: updated process bigraph version and fixed deps
b15eb14
@AlexPatrie
chore: refactored for counts and concentrations in copasi process
ffea2d3
@AlexPatrie
chore: added concentration vs counts
978b287
@AlexPatrie
chore: added plot output example
f9a383a
@AlexPatrie
feat: added viz
e5fd489
@AlexPatrie
updated for select obsv type
09a2365
@AlexPatrie
updates minor
9d4463f
@AlexPatrie
feat: updated composition method
a7205bd
@AlexPatrie
chore: checkpoint save
b3e4c5e
@AlexPatrie
feat: added schemas for handling simulation validation score
dbcacf8
@AlexPatrie
chore: update
5055b5e
@AlexPatrie
fix: added bracket
ab9b9af
@AlexPatrie
feat: setup for shared simulator instance attribute dict
3a4a042
@AlexPatrie
feat: updated processes to handle multiple simulators
80e0542
@AlexPatrie
updated simulator comparison doc instance
d54ea15
@AlexPatrie
chore: checkpoint save to be removed
e6978b6
@AlexPatrie
chore: removed unused test
5ef49e7
@AlexPatrie
feat: added comparison_api content
aac442e
@AlexPatrie
fix: updated readme for server
67db607
@AlexPatrie
fix: updated base model implementation for datamodel
fe594d1
@AlexPatrie
feat: generated spec for compare_api
eb544dd
@AlexPatrie
chore: revert dep override for local setup
0beb103
@AlexPatrie
fix: updated query params for main funcs
37395c2
@AlexPatrie
fix: minor updates
7917bda
@AlexPatrie
minor refactor
06c5617
AlexPatrie added 25 commits May 1, 2024 13:00
@AlexPatrie
feat: implemented genetic param search mockup
06a6932
@AlexPatrie
checkpoint save
8a0a234
@AlexPatrie
feat: major refactor of library structure and content
11259fb
@AlexPatrie
major refactor of library structure for unused content
c8473f2
@AlexPatrie
refactor and update savepoint
642919d
@AlexPatrie
feat: started amici process mockup
f703dcf
@AlexPatrie
feat: added amici process implementation
f74cbee
@AlexPatrie
fix: fixed readme package ref
8583c34
@AlexPatrie
savepoint
ad114f1
@AlexPatrie
update save point
b694650
@AlexPatrie
feat: added general ode process document maker
363412d
@AlexPatrie
feat: added get and set for initial species vals in amici solver and …
5a1c61e 
…updates
@AlexPatrie
feat: added process interface implementation to amici process methods
2adcfce
@AlexPatrie
updated data model and compare api content
a394e59
@AlexPatrie
feat: added qiskit process for sbml integration
0dfccae
@AlexPatrie
feat: added qiskit processes for relevant biosimulator processes
5e5dad0
@AlexPatrie
feat: updated qaoa process implementation
5127050
@AlexPatrie
feat: updated process implementation for qiskit
34024d0
@AlexPatrie
chore: savepoint
f97da76
@AlexPatrie
chore: added playground notebook scratch book to gitignore
2c53f21
@AlexPatrie
feat: added simulators mapping to ode comparison document
52e2808
@AlexPatrie
chore: cleanup of registration in initi
bd078f7
@AlexPatrie
fix: resolved incorrect emitter declaration within document
3aaf0e1
@AlexPatrie
feat: updated ode comparison document for typing and spec
623b154
@AlexPatrie
chore: savepoint update
4935fce
@AlexPatrie AlexPatrie merged commit aa28d71 into main May 7, 2024
@AlexPatrie AlexPatrie deleted the updates branch May 30, 2024 17:33
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@AlexPatrie