From 70597d6299f03b06bb9812860f93afe114c6f55c Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 28 Nov 2024 10:34:00 +0100
Subject: [PATCH] Doc: Include hdf5 functions in Python API doc

* requires libhdf5 on RTD
* exclude developer info from API doc
* minor other doc fixes
---
 .readthedocs.yml                                             | 1 +
 documentation/cpp_installation.rst                           | 1 +
 include/amici/solver.h                                       | 3 ++-
 python/examples/example_steadystate/ExampleSteadystate.ipynb | 4 ++--
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 23cc6addeb..9b63ce6dce 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -21,6 +21,7 @@ build:
   os: "ubuntu-22.04"
   apt_packages:
     - libatlas-base-dev
+    - libhdf5-serial-dev
     - swig
   tools:
     python: "3.11"
diff --git a/documentation/cpp_installation.rst b/documentation/cpp_installation.rst
index a7165ce83a..7e464122b7 100644
--- a/documentation/cpp_installation.rst
+++ b/documentation/cpp_installation.rst
@@ -18,6 +18,7 @@ Prerequisites:
 * a C++17 compatible compiler
 * a C compiler
 * Optional:
+
   * HDF5 libraries
   * boost for serialization
 
diff --git a/include/amici/solver.h b/include/amici/solver.h
index f7cde1efa0..84eb479cf6 100644
--- a/include/amici/solver.h
+++ b/include/amici/solver.h
@@ -39,7 +39,8 @@ namespace amici {
  * variables and status flags) are specified as mutable and not included in
  * serialization or equality checks. No solver setting parameter should be
  * marked mutable.
- *
+ */
+/*
  * NOTE: Any changes in data members here must be propagated to copy ctor,
  * equality operator, serialization functions in serialization.h, and
  * amici::hdf5::(read/write)SolverSettings(From/To)HDF5 in hdf5.cpp.
diff --git a/python/examples/example_steadystate/ExampleSteadystate.ipynb b/python/examples/example_steadystate/ExampleSteadystate.ipynb
index 147ae473b6..5e55114de4 100644
--- a/python/examples/example_steadystate/ExampleSteadystate.ipynb
+++ b/python/examples/example_steadystate/ExampleSteadystate.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# SBML import, observation model, sensitivity analysis, data export and visualization\n",
     "\n",
-    "This is an example using the [model_steadystate_scaled.sbml] model to demonstrate:\n",
+    "This is an example using the [model_steadystate_scaled.xml] model to demonstrate:\n",
     "\n",
     "* SBML import\n",
     "* specifying the observation model\n",
@@ -988,7 +988,7 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": "The provided measurements can be visualized together with the simulation results by passing the `Expdata` to `amici.plotting.plot_observable_trajectories`:"
+   "source": "The provided measurements can be visualized together with the simulation results by passing the `ExpData` to `amici.plotting.plot_observable_trajectories`:"
   },
   {
    "cell_type": "code",