diff --git a/python/examples/example_jax_petab/ExampleJaxPEtab.ipynb b/python/examples/example_jax_petab/ExampleJaxPEtab.ipynb index 9151cfcc13..10369f74b0 100644 --- a/python/examples/example_jax_petab/ExampleJaxPEtab.ipynb +++ b/python/examples/example_jax_petab/ExampleJaxPEtab.ipynb @@ -21,7 +21,7 @@ "\n", "To begin, we will import a model using [PEtab](https://petab.readthedocs.io). For this demonstration, we will utilize the [Benchmark Collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab), which provides a diverse set of models. For more information on importing PEtab models, refer to the corresponding [PEtab notebook](https://amici.readthedocs.io/en/latest/petab.html).\n", "\n", - "In this tutorial, we will import the Böhm model from the Benchmark Collection. Using [amici.petab_import](https://amici.readthedocs.io/en/latest/generated/amici.petab_import.html#amici.petab_import.import_petab_problem), we will load the PEtab problem. To create a [JAXModel](https://amici.readthedocs.io/en/latest/generated/amici.jax.html#amici.jax.JAXModel) instead of a standard AMICI model, we set the `jax` parameter to `True`. As we won't use the corresponding AMICI model, we set the `compile_` to `False`.\n" + "In this tutorial, we will import the Böhm model from the Benchmark Collection. Using [amici.petab_import](https://amici.readthedocs.io/en/latest/generated/amici.petab_import.html#amici.petab_import.import_petab_problem), we will load the PEtab problem. To create a [JAXModel](https://amici.readthedocs.io/en/latest/generated/amici.jax.html#amici.jax.JAXModel) instead of a standard AMICI model, we set the `jax` parameter to `True`.\n" ] }, { @@ -52,7 +52,7 @@ "# Import the PEtab problem as a JAX-compatible AMICI model\n", "jax_model = import_petab_problem(\n", " petab_problem,\n", - " compile_=False, # do not compile regular amici model\n", + " compile_=True, # do not compile regular amici model\n", " verbose=False, # no text output\n", " jax=True, # return jax model\n", ")" @@ -977,7 +977,10 @@ "\n", "# Import the PEtab problem as a standard AMICI model\n", "amici_model = import_petab_problem(\n", - " petab_problem, compile_=True, verbose=False, jax=False\n", + " petab_problem,\n", + " compile_=False, # do not recompile\n", + " verbose=False,\n", + " jax=False, # load the amici model this time\n", ")\n", "\n", "# Configure the solver with appropriate tolerances\n", diff --git a/python/sdist/pyproject.toml b/python/sdist/pyproject.toml index c2a20fd0f2..6441ac3300 100644 --- a/python/sdist/pyproject.toml +++ b/python/sdist/pyproject.toml @@ -129,9 +129,7 @@ line-length = 79 [tool.ruff] line-length = 79 extend-include = ["*.ipynb"] -exclude = ['jax.template.py'] -extend-select = ["UP"] [tool.ruff.lint] -extend-select = ["B028"] +extend-select = ["B028", "UP"] ignore = ["E402", "F403", "F405", "E741"]