AMICI v0.11.19

New:

• Added support for observable transformations (lin/log/log10) (#1567). Thereby supporting additional noise distributions in combination with least squares solvers.

Fixes:

• Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (#1541)
• Fixed a bug where argument outdir in ODEExporter.__init__ would not be used (#1543)

Other:

• Improve checking support for SBML extensions (#1546)
• SBML import: Use more descriptive IDs for flux expressions (#1551)
• Optimized SUNMatrixWrapper functions (#1538)
• C++: Changed test suite from CppUTest to gtest (#1532)
• Add CITATION.cff (#1559)
• Updated documentation (#1563, #1554, #1536)
• Removed distutils dependency (#1557)
• Require sympy<1.9

AMICI v0.11.18

New:

• Allow specifying maximum integration time via
  amici::Solver::setMaxTime() (#1530)
• Py: Add failfast and num_threads argument to simulate_petab
  (#1528, #1524)
• Enable typehints / static type checking for AMICI-generated model modules
  (#1514) (amici.ModelModule, available with Python>=3.8)

Fixes:

• Python: Fix unused argument generate_sensitivity_code in pysb2amici
  (#1526)
• Python: Fix C(++) stdout redirection which could have let to deadlocks in
  exotic situations (#1529)
• Py: Fixed deprecation warning (#1525)
• Py: Proper typehints for SWIG interface (#1523), enabling better static type
  checking and IDE integration (available with Python>=3.9)
• C++: Fixed clang compiler warning (#1521)
• C++: Fix inherited variadic ctor in exception class (#1520)
• PEtab: More informative output for unhandled species overrides (#1519)
• Return SbmlImporter from PEtab model import (#1517)

AMICI v0.11.17

Fixes:

• Fix "maybe-uninitialized" compiler warning (#1495)
• Fix substitution of expressions in `drootdt_total (#1512)
• C++: Fix serialization and == operator (#1493)
• C++: Avoid w in root and stau headers (refactor) (#1503)

Documentation:

• Updated OpenBLAS Windows installation instructions (#1496)
• Updated how-to-cite to Bioinformatics paper (#1499)
• Updated list of papers using AMICI (#1509)

Other:

• Remove sllh computation from petab_objective.simulate_petab (#1498)
• Add main.py to Python package to provide info on AMICI installation
  via python -m amici (#1500)

AMICI v0.11.16

Fixes:

• Fixed serialization bug (#1490)

New:

• Construction of condition specific plist for parameter mappings (#1487, #1488)
• Add support for error residuals (#1489)

AMICI v0.11.15

Fixes:

• Fixed initial state sensitivities in adjoint preequilibration (#1468)
• Fixed various model import / parameter mapping issues (#1469, #1473, #1475)

New:

• New AMICI releases will automatically trigger releases at
  https://biosimulators.org/simulators/amici/latest
• Transparent logo

AMICI v0.11.14

New features:

• Python model import now supports SBML Events (#1443)
• Implement support for compilation without sensitivities (#1454)

Fixes:

• Issue #1446: Check whether constant parameters are valid targets (#1450)
• Issue #1422: Fix Steadystate solver failing if preequilibration starts in
  steadystate (#1461)
• Issue #1401: Ensure diagnostics variables in ReturnData are always of
  expected length (#1438, #1447)
• Fix FIM approximation for parameter dependent sigma (#1441)
• Fix invalid SBML in PEtab/PySB import (#1433)
• Fix: No context for inspect.getouterframes (#1432)

Documentation:

• Added this CHANGELOG
• Added feature request issue template (#1437)
• Updated reference list (#1430)
• Overhauled experimental conditions notebook (#1460)

CI:

• Test Matlab interface on GHA (#1451)
• Include componentTags in SBML test suite output (#1462)
• Split SBML semantic test suite into multiple jobs (#1452)
• Fix Crauste ref val, fixes #1458 (#1459)

Misc:

• Various cleanup (#1465, #1448, #1455)
• Optimize SUNMatrixWrapper::transpose (#1439)
• Remove constant triggers from roots in Heaviside (#1440)

AMICI v0.11.13

Breaking changes:

• AMICI requires Python>=3.7
• Updated package installation (PEP517/518):
  Creating source distributions requires https://github.com/pypa/build (#1384)
  (but now handles all package building dependencies properly)

Features:

• More flexible state reinitialization (#1417)

Updated dependencies:

• Upgrade to sundials 5.7.0 (#1392)

Fixes:

• Python: account for heaviside functions in expressions (#1382)
• Python: allow loading of existing models in import_petab_problem (#1383)
• Python: Don't override user-provided compiler/linker flags (#1389)
• Python: PEtab import reinitialization fixes (#1417)
• Python: Fix PEtab observables for pysb models (#1390)
• Python: Substitute expressions in event condition expressions (#1404)
• Python: Unspecified initial states in PEtab conditions table default to SBML initial value (#1397)
• C++: Fix timepoint out of bounds access (#1402)
• C++: Fix exported CMake config (#1388)
• Fixed Dockerfile: add python3-venv (#1398, #1408)

Other:

• Slim exported swig interface (#1425)
• Updated documentation
  • Getting started tutorial (#1423)
  • List supported SBML test tags (#1428)
  • Add AMICI C++/Python/Matlab feature comparison (#1409)
  • ...
• Various minor CI improvements
• ...

AMICI v0.11.12

Features:

• Add expression IDs and names to generated models (#1374)

Fixes:

• Raise minimum sympy version to 1.7.1 (Closes #1367)
• Fix species assignment rules in reactions (#1372)
• Fix id vector for DAEs (#1376)

Docs:

• Update how-to-cite (#1378)

AMICI v0.11.11

Python

• Restore support for species references (#1358)
• Add support for noise models in pysb (#1360)
• Proper handling of discontinuities in the ODE rhs (#1352)
• Fix directly calling AMICI from snakemake (#1348 )
• Extend mathml function support, particularly for numerical arguments (#1357)
• Restore support for sympy 1.6 (#1356)

C++

• Fix some compiler related warnings (#1349, #1362 )
• Fix a rare segfault for adjoint sensitivities (#1351)

CI

• Move windows tests to GHA (#1354)
• Pin breathe to 4.24.1

Docker

• Update ubuntu to 20.04

AMICI v0.11.10

Bugfix release that restores compatibility with sympy 1.7