Support for regulatory networks (#404)

* add support for regnet now that mira has been fixed * lint * uncomment other mistakenly commented tests * swap out dict access for explicit iteration * lint
ciemss · Nov 2, 2023 · 6c6d8ee · 6c6d8ee
1 parent c5eaaac
commit 6c6d8ee
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diff --git a/pyciemss/mira_integration/compiled_dynamics.py b/pyciemss/mira_integration/compiled_dynamics.py
@@ -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()]

diff --git a/setup.cfg b/setup.cfg
@@ -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

diff --git a/tests/fixtures.py b/tests/fixtures.py
@@ -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",
 ]