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",