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updating process constructor configurations #4

Merged
merged 56 commits into from
Feb 26, 2024
Merged

updating process constructor configurations #4

merged 56 commits into from
Feb 26, 2024

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AlexPatrie
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What does this PR do?:

  • Implements changes from the biosimulators fork of this repo.
  • Updates Process implementation constructor configurations to expand scope of instantiation.
  • Minor reformatting.
  • Several updates to content housed within the scripts library.

How was this PR tested?:

  • Docker build process
  • pytest

AlexPatrie and others added 30 commits February 22, 2024 15:56
@AlexPatrie
chore: removed docker comments
922a7bd
@AlexPatrie
removed comment from pyproject
5a35207
@AlexPatrie
added biomodels yaml examples in spec library
df530e0
@AlexPatrie
updated spec
8945381
@AlexPatrie
updated composer-api library and spec
25965be
@AlexPatrie
updated composer spec
088c07e
@AlexPatrie
updated composer spec for operation ids
b4a7709
@AlexPatrie
updated scripts and poetry env in container
2d81a01
@AlexPatrie
updated container script
a7e9005
@AlexPatrie
updated container script for updated simulators spec
8c5b54a
@AlexPatrie
added write config func
b3d0daf
@AlexPatrie
updated dockerfile maker
9e27ea9
@AlexPatrie
updated docker config
54870af
@AlexPatrie
fix: removed new line delim
387e321
@AlexPatrie
updated dockerfile maker
532fa0f
@AlexPatrie
chore: added docstring and Docker import
84978ed
@AlexPatrie
chore: added docker dep to pyproject file
d7d5252
@AlexPatrie
created client for Docker in container.py
fc5bc10
@AlexPatrie
Update container.py
ad8c144
@AlexPatrie
Update container.py for running
7089648
@AlexPatrie
updated dockerfile base
058fab5
@AlexPatrie
updated container script for install
14482f5
@AlexPatrie
updated container logic
021d770
@AlexPatrie
updated script to install with poetry within the container for versio…
47bbc13 
…n control
@AlexPatrie
minor reformat of base dockerfile
d1898b9
@AlexPatrie
updated script for docker build
e6e1311
@AlexPatrie
updated script to tempfile for container
df93a48
@AlexPatrie
feat: implemented dockerfile gen path
c4efdd9
@AlexPatrie
added to does for container.py
79f287d
@AlexPatrie
Update container.py
f595d8c
@AlexPatrie
updated readme and refactored for container package
9d1dabc
@AlexPatrie
updated library for exec and io files
93299cf
@AlexPatrie
updated exec and container files chore
b7c2ffd
@AlexPatrie
feat: implemented run container pipeline for dynamic container
ce3491a
@AlexPatrie
updated exec container script for feature
c49b73c
@AlexPatrie
refactored libs and files
584b369
@AlexPatrie
updated dockerfile to include pyproject and lock
3c2e0ac
@AlexPatrie
added notebooks library and adjusted dockerfile for specific copy
9cf767c
@AlexPatrie
updated dockerfile to remove manual libnuml and added to lock file
0fe1300
@AlexPatrie
chore: added comment option for numl
b719f78
@AlexPatrie
added path insert for notebook repo access and added basic copasi use…
5f55d5c 
… in notebook
@AlexPatrie
added jupyteruser and cmd in dockerfile with volume example
e82c893
@AlexPatrie
refactored dockerfile for optimizing build
27db134
@AlexPatrie
updated dockerfile for chmod and copasi process
f8fe251
@AlexPatrie
fix: removed chmod notebooks temporarily
a3b0797
@AlexPatrie
cleaned up dockerfile and added specific dir copy
f676f8a
@AlexPatrie
added notebook truster script and spec to dockerfile
2f8134e
@AlexPatrie
fixed path in script for dockerfile
cd4236c
@AlexPatrie
added buildDockerImage workflow from Biosimulators repo and adjusted …
42e9481 
…trust notebooks remove
@AlexPatrie
removed workflow temp
390321b
@AlexPatrie
added workflow to gitignore and locally copied
65e8fd9
@AlexPatrie
added comments and vals to copasi process
7980f67
@AlexPatrie
updated copasi process constructor with optional default values
554f8cf
@AlexPatrie
chore: added comment for error handling in constructor
e04ce89
@AlexPatrie
chore: updated release-container script for optional run arg
55a6481
@AlexPatrie
updated copasi_process
fb6c32f
@AlexPatrie AlexPatrie merged commit b3e8189 into vivarium-collective:main Feb 26, 2024
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@AlexPatrie