Releases: AMICI-dev/AMICI
Releases · AMICI-dev/AMICI
AMICI v0.11.26
New features:
- Import of BioNetGenLanguage (BNGL) models by @FFroehlich in #1709
- Added support for observable-dependent sigmas by @dweindl, @FFroehlich in #1692
- Added support for pysb local functions by @FFroehlich in #1666
- Added experimental support for conservation laws for non-constant species to SBML import: conservation laws for non-constant species
by @stephanmg, @dweindl in #1669
Enable this feature by setting environment variableAMICI_EXPERIMENTAL_SBML_NONCONST_CLS
to any value- Allow using states eliminated by conservation laws to be used in root functions by @dweindl in #1677
- Added support for parameter-dependent conservation laws by @dweindl, @FFroehlich in #1678
- Added optional caching for symbolic simplifications in ODE export by @dilpath in #1672
- Added CLI option
--no-sensitivities
toamici_import_petab
by @dweindl in #1688
Fixes:
- SBML import: Raise in case of nested observables by @dweindl in #1690
- Sympy 1.10 compatibility by @dweindl in #1694
Full Changelog: v0.11.25...v0.11.26
AMICI v0.11.25
- Fixed a bug where
Model::setStateIsNonNegative(Model::getStateIsNonNegative())
would raise an exception in case conservation laws were enabled - by @dweindl in #1648 - Fixed a bug where
Model::setStateIsNonNegative
would be ignored in certain model expressions - by @FFroehlich in #1650 - Fixed a bug where special function parsing inside
min()
andmax()
would not be parsed correctly - by @dweindl in #1655 - Fixed a numpy dependency issues for Mac+ARM systems - by @dweindl in #1657
- Fixed convergence check in Newton method - by @plakrisenko in #1663
- Add
AMICI_CXX_OPTIONS
to pass libamici-specific compiler options during CMake-based builds - by @dweindl in #1664 - Fixed various warnings and updated documentation - by @dweindl
Full Changelog: v0.11.24...v0.11.25
AMICI v0.11.24
Features:
- Introduced environment variable
AMICI_DLL_DIRS
to control DLL directories on Windows (useful for setting BLAS library directory, as required by Python>=3.8) by @dweindl in #1637 - Dropped Python3.7 support by @dweindl in #1635
- Include header files in CMake targets for better IDE integration by @dweindl in #1639
Fixes:
- Fixed an issue in PEtab import where all-integer parameters would previously result in a TypeError by @stephanmg in #1634
- Fixed tempdir deletion issues for test suite on Windows by @dweindl in #1636
- Added functions to provide state IDs/names for x_solver by @dweindl in #1638
- Fixed docs on RTD by @dweindl in #1643
Full Changelog: v0.11.23...v0.11.24
AMICI v0.11.23
Features:
- Added overload for Model::setParameterScale with vector by @dilpath in #1614
- Removed assert_fun argument from gradient checking, improve output by @dweindl, @FFroehlich in #1609
- Added get_expressions_as_dataframe by @dweindl in #1621
- Added
id
field to ExpData and ReturnData by @dweindl in #1622 - Included condition id in dataframes by @dweindl in #1623
Fixes:
- C++: Fixed SUNMatrixWrapper ctor for size 0 matrices by @dweindl in #1608
- Python: Handle TemporaryDirectory cleanup failures on Windows by @dweindl in #1617
- Python: pysb.Model.initial_conditions throws a DeprecationWarning by @PaulJonasJost in #1620
- Fixed wrong array size in warnings by @dweindl in #1624
NOTE: AMICI 0.11.23 requires numpy<1.22.0
NOTE: This is the last release supporting Python 3.7
Full Changelog:
v0.11.22...v0.11.23
AMICI v0.11.22
- Require sympy>=1.9,pysb>=1.13.1 by @FFroehlich, @dweindl in #1599
- Fixed sympy deprecation warning by @dweindl in #1600
- Updated Windows installation instructions for Python>=3.8 by @dweindl in #1597
- Fixed plot labels by @dweindl in #1598
Full Changelog: v0.11.21...v0.11.22
AMICI v0.11.21
Fixes:
- Fixed a bug in recursion depth computation for model expressions. This may
have resulted in incorrect sensitivities for models with expressions nested
more than 2 levels. (#1595) - Fixed improper handling of Piecewise functions in PySB import which may have
produced incorrect simulation results. (#1594) - Fixed changed googletest reference which broke the CMake-based build if
tests were enabled (#1592)
New:
- It's now possible to build AMICI using Ninja (#1593)
Full Changelog: v0.11.20...v0.11.21
AMICI v0.11.20
New:
- Changed parameter mappings such that unassigned values have non-nan default values. This fixes erroneous evaluation of
llh
asNaN
in some situations (#1574) - Added support for Python 3.10 (#1555)
Fixes:
- Fixed a bug when simulation start time was not transferred when copying a solver instance (#1573)
- Fixed a bug which led to incorrect sensitivies for models with multiple assignment rules or rate rules (#1584)
Other:
- Update CI and documentation settings (#1569, #1527, #1572, #1575, #1579, #1580, #1589, #1581)
- Extend set of validated benchmark models that is checked during CI (#1571, #1577)
- Fixed string formatting in derivative checks (#1585)
- Added helper methods to save and restore model instance-only settings (#1576)
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
inODEExporter.__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
andnum_threads
argument tosimulate_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
inpysb2amici
(#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
inroot
andstau
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: