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Support for regulatory networks #404

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merged 5 commits into from
Nov 2, 2023
Merged

Support for regulatory networks #404

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fd75ac6
add support for regnet now that mira has been fixed
SamWitty Nov 2, 2023
e98b295
lint
SamWitty Nov 2, 2023
688315c
uncomment other mistakenly commented tests
SamWitty Nov 2, 2023
b1c33c6
swap out dict access for explicit iteration
SamWitty Nov 2, 2023
1200408
lint
SamWitty Nov 2, 2023
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3 changes: 1 addition & 2 deletions pyciemss/mira_integration/compiled_dynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,8 +50,7 @@ def _compile_initial_state_mira(
src: mira.modeling.Model,
) -> Callable[..., Tuple[torch.Tensor]]:
symbolic_initials = {
get_name(var): src.template_model.initials[get_name(var)].expression.args[0]
for var in src.variables.values()
get_name(var): var.data["expression"].args[0] for var in src.variables.values()
}
numeric_initial_state_func = sympytorch.SymPyModule(
expressions=[symbolic_initials[get_name(var)] for var in src.variables.values()]
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -9,7 +9,7 @@ license_files = LICENSE
install_requires =
jupyter
torch >= 1.8.0
mira @ git+https://github.com/indralab/[email protected].0
mira @ git+https://github.com/indralab/[email protected].1
chirho @ git+https://github.com/BasisResearch/chirho@f3019d4b22f4e49261efbf8da90a30095af2afbc
sympytorch
torchdiffeq
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2 changes: 1 addition & 1 deletion tests/fixtures.py
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Expand Up @@ -17,7 +17,7 @@
]

REGNET_URLS = [
# "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/regnet/examples/lotka_volterra.json",
"https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/regnet/examples/lotka_volterra.json",
# "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/main/regnet/examples/syntax_edge_cases.json",
]

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