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updated poetry lock and configs for version #5

Merged
merged 66 commits into from
Mar 1, 2024
Merged

updated poetry lock and configs for version #5

merged 66 commits into from
Mar 1, 2024

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AlexPatrie
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@AlexPatrie AlexPatrie commented Feb 26, 2024 •
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What does this PR do?:

  • Updates source code in vivarium-collective.biosimulator-processes:main.
  • Optimizes Docker build
  • Implements example notebooks in notebooks library.

@AlexPatrie
updated poetry lock and configs for version
281d1cd
@AlexPatrie
updated dockerfile and refactored processes
fe341b2
@AlexPatrie
updated dockerfile for refactor
bc9a4c2
@AlexPatrie
feat: reimplemented current copasiprocess and updated builder shell
d187cb0
@AlexPatrie
updated build container for set -e
ed3f1a5
@AlexPatrie
updated init for refactored package structure
3e783be
@AlexPatrie
updated build and init
4447889
@AlexPatrie
updated gitignore for env
2991955
@AlexPatrie
updated release to clear cache'
c835541
@AlexPatrie
finished deps in setup.py and added notebook in lock config
0f3d26e
@AlexPatrie
updated copasi process for schema and process notebook
19c0028
@AlexPatrie
updated config schema for copasi process
0ca8272
@AlexPatrie
updated copasi process comments docs and added biomodels method to pr…
d694a77 
…ocess
@AlexPatrie
updated notebook for copasi and added composer suffix to content in n…
be9ad54 
…otebook library
@AlexPatrie
updated composer api with pbg gpt analyst
50d3a72
@AlexPatrie
updated speech api datamodel
9300506
@AlexPatrie
removed composer-api library for other location
25906c6
@AlexPatrie
moved container package to builder package
18d1db6
@AlexPatrie
updated process
ab64a39
@AlexPatrie
updated copasi_process for more specific config dec:
0bbb94e
@AlexPatrie
updated copasi process docs
0c0cbff
@AlexPatrie
updated copasi docs for schema
3a05e23
@AlexPatrie
updated copasi proc docs
ae01719
@AlexPatrie
updated copasi proc docs to reflect full schema
a61cbc8
@AlexPatrie
updated copasi docs
fbb7e2d
@AlexPatrie
added units to config for copasi process schema
3463a11
@AlexPatrie
updated notebook content and added model changes type in copasi process
83cd298
@AlexPatrie
added utils file with fetch models functions and adjusted type
301f758
@AlexPatrie
slight copasi process reform in comments
e58f693
@AlexPatrie
minor refactor of model changes type dec
905387a
@AlexPatrie
tidy up of CopasiProcess script
eb3b593
@AlexPatrie
adjusted timecourse dec
7860754
@AlexPatrie
updated process for copasi notebook
4849843
@AlexPatrie
adjusted reaction in example for copasi
27f17e7
@AlexPatrie
updated initial state for conditional model parameters in constructor
e228bf5
@AlexPatrie
updated changes schema string in process_types
2dd6907
@AlexPatrie
fix: completed instance schema for working examples
277130a
@AlexPatrie
moved generate process instance func to utils
a46409b
@AlexPatrie
imported instance generator to notebook
44dad45
@AlexPatrie
added copasi process docs to utils
623983b
@AlexPatrie
added composite copasi emitter generator to utils
501693c
@AlexPatrie
updated utils generator
f2b711c
@AlexPatrie
added param scan instance
c885459
@AlexPatrie
updated sed model config schema
0b6c0e5
@AlexPatrie
updated docs in generate sed model config schema
8761175
@AlexPatrie
feat: added copasi parameter scan instance function in utils
ae00edc
@AlexPatrie
fix: minor utils refacor
39f224d
@AlexPatrie
minor
57dc4ac
@AlexPatrie
feat: added param scan to notebook
c313924
@AlexPatrie
updated utils function to implement entrypoint
bfda29c
@AlexPatrie
updated reformatting of copasi notebook
32a0192
@AlexPatrie
feat: implemented builder adjusted scripts for new smoldyn and updated l
c57e576
@AlexPatrie
fix: added builder to cobra notebook and process init
d612c3e
@AlexPatrie
fix: added python3 dev install in container
2d7c906
@AlexPatrie
udpate
a3508dd
@AlexPatrie
updated process types and added biosimulator_builder instance
fbdba63
@AlexPatrie
added granular species pydantic types
f6a031b
@AlexPatrie
refactored data_model file name
88b8ed5
@AlexPatrie
update again
237aca7
@AlexPatrie AlexPatrie merged commit 75bb234 into vivarium-collective:main Mar 1, 2024
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@AlexPatrie