Jax example notebook (#1996)

* add sllh to `simulate_petab`

* use ExpData for plist if available

* use plist if set; breakpoint at error; preliminary test

* add sensi test to preexisting benchmark model test

* remove outdated test and test cases

* add FD check for petab problems; add petab problem test case for SLLH; clean up

* typo, RTOL

* fix paths

* docs

* Apply suggestions from code review

Co-authored-by: Yannik Schälte <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>

* reviews: docstring;error handling;optional sllh aggregation

* Apply suggestions from code review

Co-authored-by: Fabian Fröhlich <[email protected]>

* review: clean up

* ignore parameters missing due to estimate=0

* add test for petab benchmark models

* use fiddy

* Create Differential Programming with JAX.ipynb

* pass model_name to _create_model_output_dir_name

fixes #1993

* update notebook

* move notebook and add to doc

* prettify notebook

* develop merge

* fix after merge

* merge conflicts

* restore changes

* make scaled gradients optional, default to linear

* adress reviewer comments

* test scaled and unscaled

* fix notebook

* fix notebook

* revert merge changes

* fix binder

---------

Co-authored-by: dilpath <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Dilan Pathirana <[email protected]>
Co-authored-by: Yannik Schälte <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>

Author: 4 people

.gitignore

@@ -154,6 +154,7 @@ python/examples/example_presimulation/model_presimulation/*
 python/examples/example_presimulation/model_presimulation_re/*
 python/examples/example_constant_species/model_constant_species_reduced/*
 python/examples/example_constant_species/model_constant_species/*
+python/examples/example_jax/amici_models/*
 python/tests/sbml_test_models/*
 python/tests/piecewise_test/*
 
@@ -200,4 +201,4 @@ Benchmark-Models-PEtab/
 CS_Signalling_ERBB_RAS_AKT/
 cache_fiddy/*
 debug/*
-tests/benchmark-models/cache_fiddy/*
+tests/benchmark-models/cache_fiddy/*

binder/Dockerfile

@@ -30,7 +30,7 @@ RUN adduser --disabled-password \
     ${NB_USER}
 USER ${NB_USER}
 RUN python3 -m pip install --upgrade build wheel setuptools pip && \
-    python3 -m pip install --no-cache-dir notebook jupyterlab jupyterhub
+    python3 -m pip install --no-cache-dir notebook jupyterlab jupyterhub jax[cpu]
 # END BINDER
 
 # BEGIN BINDER

binder/overview.ipynb

@@ -29,7 +29,11 @@
     "\n",
     "* [Simulation errors](../python/examples/example_errors.ipynb)\n",
     "\n",
-    "  Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.\n"
+    "  Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.\n",
+    "\n",
+    "* [Interfacing JAX](../python/examples/example_jax/ExampleJax.ipynb)\n",
+    "\n",
+    "  Provides guidance on how to combine AMICI with differential programming frameworks such as JAX.\n"
    ]
   }
  ],