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Fix JAX PEtab condition-table resolution: state reinit, noise distribution, and differentiability #3207

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Merged
FFroehlich merged 9 commits into from
Jul 10, 2026
Merged

Fix JAX PEtab condition-table resolution: state reinit, noise distribution, and differentiability #3207

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db00ced
Fix CI failures in JAX PEtab v1/v2 backend
FFroehlich Jul 9, 2026
4646543
Ignore another benign petab1to2 warning-turned-error
FFroehlich Jul 9, 2026
89e7b09
Fix state reinitialisation lookup and petab1to2 noise-distribution bu…
FFroehlich Jul 9, 2026
b42de7b
Resolve JAX PEtab reinitialisation values live so gradients flow
FFroehlich Jul 9, 2026
5411a21
Resolve condition-table parameter overrides live too
FFroehlich Jul 9, 2026
826d605
Apply suggestions from code review
FFroehlich Jul 9, 2026
bf387b3
Drop petab1to2 noise-distribution workaround; rely on upstream fix
FFroehlich Jul 9, 2026
72bd865
Revert unnecessary _petab_import.py changes
FFroehlich Jul 9, 2026
ab21bf9
Fix _build_simulation_df_v2: consistent masking, drop fragile sc[0] l…
FFroehlich Jul 10, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/test_petab_test_suite.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ jobs:
run: |
source ./venv/bin/activate \
&& python3 -m pip uninstall -y petab \
&& python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@44c8062ce1b87a74a0ba1bd2551de0cdc2a13ff1 \
&& python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@1b8599dd1eb9bda74853255b4cc4baf75b7e4d63 \
&& python3 -m pip install git+https://github.com/pysb/pysb@master \
&& python3 -m pip install sympy>=1.12.1

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6 changes: 3 additions & 3 deletions doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb
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Expand Up @@ -107,7 +107,7 @@
"outputs": [],
"source": [
"# # Define the simulation condition\n",
"experiment_condition = \"_petab_experiment_condition___default__\"\n",
"experiment_condition = (\"_petab_experiment_condition___default__\",)\n",
"\n",
"# # Access the results for the specified condition\n",
"ic = results[\"dynamic_conditions\"].index(experiment_condition)\n",
Expand Down Expand Up @@ -163,7 +163,7 @@
"import numpy as np\n",
"\n",
"# Define the experiment condition\n",
"experiment_condition = \"_petab_experiment_condition___default__\"\n",
"experiment_condition = (\"_petab_experiment_condition___default__\",)\n",
"\n",
"\n",
"def plot_simulation(results):\n",
Expand Down Expand Up @@ -389,7 +389,7 @@
"from amici.sim.jax import ReturnValue\n",
"\n",
"# Define the simulation condition\n",
"experiment_condition = \"_petab_experiment_condition___default__\"\n",
"experiment_condition = (\"_petab_experiment_condition___default__\",)\n",
"ic = 0\n",
"\n",
"# Load condition-specific data\n",
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10 changes: 10 additions & 0 deletions pytest.ini
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Expand Up @@ -13,6 +13,16 @@ filterwarnings =
once:Signature .* for <class 'numpy.longdouble'> does not match any known type. falling back to type probe function:UserWarning
# petab
ignore:Using petab.v1.Problem with PEtab2.0 is deprecated:DeprecationWarning
# petab1to2 warns-and-falls-back for v1-only noise distributions not
# supported in v2 (e.g. log10-normal -> log-normal); this is an
# intentional, documented conversion decision, not an error
ignore:Noise distribution .* is not supported in PEtab v2\. Using .* instead\.:UserWarning
# petab1to2 drops PEtab v1's parameterScale column when upgrading to v2
# (v2 has no equivalent); nominal/simulation values are unaffected since
# petab v1's nominalValue is always stored in linear units regardless of
# parameterScale, so this only affects estimation-scale metadata, not
# simulation correctness
ignore:Parameter scales are not supported in PEtab v2\.:UserWarning
# amici
ignore:Conservation laws for non-constant species in models with RateRules are currently not supported and will be turned off.:UserWarning
ignore:Conservation laws for non-constant species in models with Species-AssignmentRules are currently not supported and will be turned off.:UserWarning
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