Merge pull request #1956 from AMICI-dev/release_0.16.0

Release 0.16.0

.github/workflows/test_python_ver_matrix.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11']
         experimental: [false]
 
     steps:

.readthedocs.yml

@@ -24,5 +24,7 @@ build:
     # for custom doxygen
     - libclang-cpp9
     - libclang1-9
+    - libatlas-base-dev
+    - swig
   tools:
     python: "3.8"

CHANGELOG.md

@@ -2,6 +2,49 @@
 
 ## v0.X Series
 
+### v0.16.0 (2023-01-25)
+
+Features
+* Python 3.11 compatibility
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1876
+* AMICI now runs on binder (https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=binder%2Foverview.ipynb)
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1935,
+  https://github.com/AMICI-dev/AMICI/pull/1937,
+  https://github.com/AMICI-dev/AMICI/pull/1939
+* More informative `Solver.__repr__` and `ExpData.__repr__`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1928
+  and @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1948
+* `simulate_petab` returns the generated/used `ExpData`s
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1933
+* Model module is now accessible from model instance
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1932
+* Added `plot_jacobian`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1930
+* Now logs all nested execution times as debug
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1947
+* Always check for finite initial states, not only with
+  `Model.setAlwaysCheckFinite(True)`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1955
+
+Fixes
+* `ReturnDataView.status` now returns `int` instead of `float`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1929
+* Updated simulation status codes
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1931
+* Skip irrelevant frames in stacktraces
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1934
+* Fixed compiler warning (matlab)
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1954
+
+Documentation:
+* Added a notebook demonstrating common simulation failures and show how to
+  analyze / fix them
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1946
+* various minor fixes / updates
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.15.0...v0.16.0
+
+
 ### v0.15.0 (2023-01-11)
 
 Features

README.md

@@ -85,7 +85,8 @@ To install AMICI, first read the installation instructions for
 [Matlab](https://amici.readthedocs.io/en/develop/matlab_installation.html).
 
 To get you started with Python-AMICI, the best way might be checking out this
-[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb).
+[Jupyter notebook](https://github.com/AMICI-dev/AMICI/blob/master/documentation/GettingStarted.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AMICI-dev/AMICI/develop?labpath=documentation%2FGettingStarted.ipynb).
 
 To get started with Matlab-AMICI, various examples are available
 in [matlab/examples/](https://github.com/AMICI-dev/AMICI/tree/master/matlab/examples).

binder/README.md

@@ -0,0 +1,5 @@
+# binder/repo2docker configuration
+
+Configuration files for [binder](https://mybinder.org/) / repo2docker.
+
+Doc: https://mybinder.readthedocs.io/en/latest/using/config_files.html

binder/apt.txt

@@ -0,0 +1,5 @@
+clang
+libatlas-base-dev
+libboost-serialization-dev
+libhdf5-serial-dev
+swig

binder/overview.ipynb

@@ -0,0 +1,47 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "f7ebed12-4309-4c92-a54e-da80ccd2d5e7",
+   "metadata": {},
+   "source": [
+    "# AMICI example notebooks\n",
+    "\n",
+    "* [Getting started](../documentation/GettingStarted.ipynb)\n",
+    "\n",
+    "  Brief intro to AMICI for first-time users.\n",
+    "\n",
+    "* [Example \"steadystate\"](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
+    "\n",
+    "  A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
+    "\n",
+    "* [PEtab import / simulation](../python/examples/example_petab/petab.ipynb)\n",
+    "\n",
+    "  How to import and simulate PEtab problems.\n",
+    "\n",
+    "* [Experimental conditions](../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb)\n",
+    "\n",
+    "  How to represent different experimental conditions in AMICI and how to use preequilibration.\n",
+    "\n",
+    "* [Steadystate (sensitivities)](../python/examples/example_constant_species/ExampleEquilibrationLogic.ipynb)\n",
+    "\n",
+    "  Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities.\n",
+    "\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"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

binder/postBuild

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -eou pipefail
+
+pip install -e "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab"
+pip install -e python/sdist[petab,pysb]
+
+scripts/buildBNGL.sh

binder/runtime.txt

@@ -0,0 +1 @@
+python-3.10

binder/start

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -eou pipefail
+
+export BNGPATH="$(pwd)/ThirdParty/BioNetGen-2.7.0"
+
+exec "$@"