AMICI v0.11.8

Python

• Fix pysb-petab support (#1288)
• Fix ExpData constructor overloading (#1299)
• Fix support for positivity enforcement (#1306)
• Refactor SBML import, adds support for parameter rate rules and initial assignments (#1284, #1296, #1304)
• Improve model generation for models with many parameters (#1300)
• Add support for PEtab based synthetic data generation (#1283)

C++

• Make HDF5 an optional dependency (#1285)

Doc

• General Improvements to Documentation (#1289, #1291, #1292, #1293, #1294, #1286, #1277, #1281)

CI

• Add python 3.9 support test (#1282)
• Allow manual triggering of GitHub actions (#1287)
• Remove appveyor config (#1295)
• Update GHA env and path management (#1302)

AMICI v0.11.7

Python

• Improve and extend available objective functions (#1235)
• Fix processing of compartment definitions (#1223)
• Fix replacement of reserved symbols (#1265)
• Use Hierarchical Derivatives for Expressions (#1224, #1246)
• Fix duplicate running of swig (#1216)
• Overload python interface functions for amici.{Model,Solver,ExpData} and amici.{Model,Solver,ExpData}Ptr (#1271)

C++

• Fix and extend use of sparse matrix operations (#1230, #1240, #1244, #1247, #1271)
• Fix application of maximal number of steps, MaxNumStep parameter now limit total number of steps, not number of steps between output times. (#1267)

Doc

• Move all Documentation to RTD (#1229, #1241)
• General Improvements to Documentation (#1225, #1227, #1219, #1228, #1232, #1233, #1234, #1237, #1238, #1239, #1243, #1253, #1255, #1262)

CI

• Better check for doc building (#1226)
• Add more gradient checks (#1213)
• Update GHA to Ubuntu 20.04 (#1268)

AMICI v0.11.6

Python

• Bugfix for piecewise functions (#1199)
• Refactor swigging - generate one single wrapper (#1213)

C++

• Fix warnings: account for zero indexing in nan/inf error (#1112)

Doc

• Update Windows build instructions (#1200, #1202)
• Update README: Projects using AMICI (#1209)
• Add CODE_OF_CONDUCT.md (#1210)
• Update documentation for Python interface (#1208)

CI

• Create sdist on GHA using swig4.0.1 (#1204) (Fixing broken pypi package)
• Fix links after repository move
• Speed-up swig build: disable all languages except python (#1211)
• Fix doc generation on readthedocs (#1196)

AMICI v0.11.5

General

• Move repo to new organization (#1193)
• Update Bibliography

Python

• Fix bug for energyPySB models (#1191)

CI

• Fix release deployment (#1189)

AMICI v0.11.4

Python

• Skip unnecessary expressions in pysb models (#1185)
• MSVC compiler support (this time for real... #1152)

CI

• Implement MSVC tests (#1152)
• Rename and group GitHub actions (#1186)
• Fix release deployment (#1186)

AMICI v0.11.3

Python

• Fix simplification for pysb models (#1168)
• Pass verbosity flags to pysb network generation (#1173)
• Enable experimental pysb-petab support (#1175)
• Add installation instructions for Fedora (#1177)
• Implement support for SBML rate-references (#1180)

C++

• Refactoring (#1162, #1163)

CI

• Move majority of tests to Github Actions (#1166, #1160)
• Improve reporting of skipped tests in SBML testsuite (#1183)

AMICI v0.11.2

Python

• Speed up model import, compilation (#1123, #1112)
• Improve/Add steady-state solver documentation (#1102)
• Improve extension import (#1141)
• Bugfixes SBML import (#1135, #1134, #1145, #1154)
• Fixed issue that prevented simplification (#1158)

C++

• Bugfixes (#1121, #1125, #1131, #1132, #1136)
• Enable openMP by default (#1118)
• Improve memoy footprint for simulations with replicates (#1153)
• Improve steady-state solver and add option to to adjoint-steadystate hybrid (#1143, #1099, #1129, #1146)

CI

• Store build artifacts from github actions (#1138)

AMICI v0.11.1

Python

• Upgrade to sympy 1.6.0, which is now required minimum version (#1098, #1103)
• Speed up model import
  • Speed-up computation of sx0, reduce file size (#1109)
  • Replace terribly slow sympy.MutableDenseMatrix.is_zero_matrix by custom implementation (#1104)
• speedup dataframe creation in get*AsDataFrame (#1088)
• Allow caching edatas for simulate_petab (#1106)
• Fix wrong deprecation warning (Fixes #1093)
• Fix segmentation faults in NewtonSolver under certain conditions (#1089, #1090, #1097)
• fix wrong power function call in unscale_parameter (#1094)
• Fix MathML conversion (#1086)
• Fix deepcopy of SymPy objects (#1091)

Matlab

• handle empty rdata->{pre|post}eq_numlinsteps (Closes #1113), which previously made the matlab interface unusable
• Fix generation of compileMexFile.m for matlab compilation of python code (#1115)

C++

• Reduce memory requirements and speedup compilation of large models (#1105)
• Place generated code into own namespace (#937) (#1112)
• Fix several msvc compiler warnings (#1116) (Note that MSVC support is still experimental) breaking change for users of C++ interface
• Fix swig warning: ensure base class ContextManager is known before use (Fixes #1092) (#1101)

CI

• Don't install/run valgrind on travis CI (done with github actions… (#1111)

AMICI v0.11.0

Python:

• Implement support for variable compartments (#1036)
• Better handling of constant species (#1047)
• Better handling of C++ enums, this makes amici.SensitivityMethod_forward available as amici.SensitivityMethod.forward (#1042)
• Improve installation routines (#1055, #1056, #1058, #1076)
• Add option to reduce memory usage (#1044)
• Fix handling of symbolic expressions in nested rules (#1081, 1069)

Library:

• Update Sundials to 5.2.0 (#1039)
• Update SuiteSparse to 5.4.0 (#1040)
• Refactor use of ReturnData, now completely created post-hoc (#1002)
• Fix propagation of reinitialization in ExpData constructor (#1041)
• Fix issue where InternalSensitivityParameter was sometimes not set (#1075)
• Fix or disable certain combinations of equilibraition, presimulation and adjoint sensitivity analysis

CI:

• Move from Codacy to Sonarcloud (#1065)
• Run SBML Testsuite when appropriate (#1058)

AMICI v0.10.21

Library:

• Fix: Handle paths with blanks in build scripts
• Feature: Add function to write amici::Solver settings to HDF5 (#1023)
• Fix: typehints (#1018, #1022)
• Refactor: Move creation of parameter mapping for objective<->simulation to classes (#1020)

CI:

• Refactor: Cleanup and reorganize tests (#1026)
• Fix: benchmark problem test should fail on missing files (Closes #1015)