Update API page

doc/api.rst

@@ -1,12 +1,36 @@
 PEtab SciML Python API
-=======================
+======================
 
-.. rubric:: Modules
+Standard
+--------
+
+Read, write, and validate the PEtab SciML array data and neural network YAML
+files.
+
+.. autosummary::
+   :toctree: generated
+
+   petab_sciml.standard.ArrayData
+   petab_sciml.standard.ArrayDataStandard
+   petab_sciml.standard.NNModel
+   petab_sciml.standard.NNModelStandard
+   petab_sciml.standard.Input
+   petab_sciml.standard.add_array_files_to_yaml
+   petab_sciml.standard.extract_nn_yaml_parameters
+   petab_sciml.standard.extract_torch_parameters
+
+   petab_sciml.standard.nn_model
+   petab_sciml.standard.array_data
+
+Problem utilities
+-----------------
+
+Helpers for constructing common PEtab SciML problem types from their
+components.
 
 .. autosummary::
    :toctree: generated
    :recursive:
 
-   petab_sciml
-   petab_sciml.standard
+   petab_sciml.problem_utils.neural_ode
    petab_sciml.problem_utils

doc/conf.py

@@ -2,7 +2,6 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-from __future__ import annotations
 
 import inspect
 

doc/examples/getting_started/requirements.txt

@@ -17,7 +17,7 @@ bleach==6.2.0
 certifi==2025.8.3
 cffi==2.0.0
 charset-normalizer==3.4.3
-chex==0.1.91
+chex==0.1.90
 cmake==4.1.0
 cmake-build-extension==0.6.0
 colorama==0.4.6
@@ -97,15 +97,15 @@ notebook==7.4.5
 notebook_shim==0.2.4
 numpy==2.2.3
 opt_einsum==3.4.0
-optax==0.2.6
+optax==0.2.5
 optimistix==0.0.10
 oyaml==1.0
 packaging==25.0
 pandas==2.3.2
 pandocfilters==1.5.1
 parso==0.8.5
 petab @ git+https://github.com/petab-dev/libpetab-python.git@99373c4340512def5a23bf2a75805c3f88251251
-petab_sciml @ git+https://github.com/PEtab-dev/petab_sciml.git@80af726a3c2e430a068ea1ebf567f77c072fd85f#subdirectory=src/python
+petab_sciml @ git+https://github.com/PEtab-dev/petab_sciml.git@main
 pexpect==4.9.0
 pillow==11.3.0
 Pint==0.25