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Migrate fiddy adapter onto the redesigned fiddy engine #3248

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Merged
dweindl merged 11 commits into from
Sep 9, 2026
Merged

Migrate fiddy adapter onto the redesigned fiddy engine #3248

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e62a1d8
Migrate fiddy adapter onto the redesigned fiddy engine
dweindl Sep 5, 2026
2f41490
Wire bounds-aware clamping into PEtab benchmark gradient checks
dweindl Sep 6, 2026
d9c4d7b
Fix JAX benchmark CI job installing a stale fiddy branch
dweindl Sep 6, 2026
5184ea9
Remove settings that only worked around a now-fixed fiddy tolerance gap
dweindl Sep 6, 2026
e37fccb
Test that JoblibExecutor agrees with SequentialExecutor on a real model
dweindl Sep 8, 2026
dd537b8
Treat AMICI's structurally-empty rdata fields as absent in the fiddy …
dweindl Sep 8, 2026
8ddd876
Fail clearly when pickling a Solver without HDF5 support; skip test o…
dweindl Sep 8, 2026
dec9d6e
Fix ExpData.free_parameters guard blocking any amici_edata usage
dweindl Sep 8, 2026
7d7ee08
Resolve fiddy derivative parameter axis from rdata.plist, add output_…
dweindl Sep 8, 2026
b33ba65
Install fiddy from main now that the FD-engine redesign is merged
dweindl Sep 8, 2026
cfc2f06
less bla
dweindl Sep 8, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/test_benchmark_collection_models.yml
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Expand Up @@ -163,7 +163,7 @@ jobs:
run: |
python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@1b8599dd1eb9bda74853255b4cc4baf75b7e4d63 \
&& python3 -m pip install -U sympy \
&& python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@amici100
&& python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@main

- run: pip uninstall -y diffrax && pip install git+https://github.com/patrick-kidger/diffrax@main # TODO FIXME https://github.com/patrick-kidger/diffrax/issues/654 + event dirs

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5 changes: 5 additions & 0 deletions .github/workflows/test_windows.yml
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Expand Up @@ -58,6 +58,11 @@ jobs:
shell: bash
run: pip install -v $(ls -t dist/amici-*.tar.gz | head -1)[petab,test,jax]

# TODO: switch back to PyPI once the fiddy redesign is released
- name: Install fiddy from GitHub
shell: bash
run: pip install git+https://github.com/ICB-DCM/fiddy.git@main

- run: python -m amici

- name: Get Pooch Cache Directory
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,12 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni

### v1.1.1 (unreleased)

**Features**

* The `fiddy` adapter (`amici.adapters.fiddy`) and the `fiddy` package itself
were redesigned, making finite-difference gradient checks much more
robust and requiring few, if any, hyperparameters.

**Fixes**

* There are no more reserved names: previously, model import or
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