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Merge pull request #1956 from AMICI-dev/release_0.16.0
Release 0.16.0
2 parents 0859bde + 3aa4579 commit ed36b2d

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‎.github/workflows/test_python_ver_matrix.yml‎

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strategy:
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fail-fast: false
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matrix:
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python-version: [3.8, 3.9, '3.10']
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python-version: [3.8, 3.9, '3.10', '3.11']
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experimental: [false]
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steps:

‎.readthedocs.yml‎

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# for custom doxygen
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- libclang-cpp9
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- libclang1-9
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- libatlas-base-dev
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- swig
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tools:
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python: "3.8"

‎CHANGELOG.md‎

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## v0.X Series
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### v0.16.0 (2023-01-25)
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Features
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* Python 3.11 compatibility
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1876
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* AMICI now runs on binder (https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb)
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1935,
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https://github.com/AMICI-dev/AMICI/pull/1937,
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https://github.com/AMICI-dev/AMICI/pull/1939
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* More informative `Solver.__repr__` and `ExpData.__repr__`
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1928
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and @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1948
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* `simulate_petab` returns the generated/used `ExpData`s
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1933
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* Model module is now accessible from model instance
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1932
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* Added `plot_jacobian`
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1930
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* Now logs all nested execution times as debug
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by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1947
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* Always check for finite initial states, not only with
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`Model.setAlwaysCheckFinite(True)`
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1955
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Fixes
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* `ReturnDataView.status` now returns `int` instead of `float`
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1929
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* Updated simulation status codes
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1931
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* Skip irrelevant frames in stacktraces
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1934
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* Fixed compiler warning (matlab)
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1954
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Documentation:
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* Added a notebook demonstrating common simulation failures and show how to
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analyze / fix them
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1946
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* various minor fixes / updates
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**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.15.0...v0.16.0
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### v0.15.0 (2023-01-11)
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Features

‎README.md‎

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[Matlab](https://amici.readthedocs.io/en/develop/matlab_installation.html).
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To get you started with Python-AMICI, the best way might be checking out this
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[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb).
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[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb)
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=documentation%2FGettingStarted.ipynb).
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To get started with Matlab-AMICI, various examples are available
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in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).

‎binder/README.md‎

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# binder/repo2docker configuration
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Configuration files for [binder](https://mybinder.org/) / repo2docker.
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Doc: https://mybinder.readthedocs.io/en/latest/using/config_files.html

‎binder/apt.txt‎

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clang
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libatlas-base-dev
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libboost-serialization-dev
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libhdf5-serial-dev
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swig

‎binder/overview.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "f7ebed12-4309-4c92-a54e-da80ccd2d5e7",
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"metadata": {},
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"source": [
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"# AMICI example notebooks\n",
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"\n",
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"* [Getting started](../documentation/GettingStarted.ipynb)\n",
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"\n",
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" Brief intro to AMICI for first-time users.\n",
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"\n",
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"* [Example \"steadystate\"](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
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"\n",
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" A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
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"\n",
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"* [PEtab import / simulation](../python/examples/example_petab/petab.ipynb)\n",
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"\n",
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" How to import and simulate PEtab problems.\n",
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"\n",
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"* [Experimental conditions](../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
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"\n",
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" How to represent different experimental conditions in AMICI and how to use preequilibration.\n",
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"\n",
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"* [Steadystate (sensitivities)](../python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb)\n",
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"\n",
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" Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities.\n",
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"\n",
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"* [Simulation errors](../python/examples/example_errors.ipynb)\n",
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"\n",
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" Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.\n"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "",
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"name": ""
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},
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"language_info": {
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"name": ""
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎binder/postBuild‎

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#!/bin/bash
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set -eou pipefail
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pip install -e "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab"
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pip install -e python/sdist[petab,pysb]
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scripts/buildBNGL.sh

‎binder/runtime.txt‎

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python-3.10

‎binder/start‎

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#!/bin/bash
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set -eou pipefail
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export BNGPATH="$(pwd)/ThirdParty/BioNetGen-2.7.0"
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exec "$@"

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