Changelog
v0.X Series
v0.11.27 (2022-04-04)
New features:
Checking condition number when computing sensitivities via Newton by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1730
Removed SPBCG solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1729
Added Newton step convergence checks to steadystate solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1737
Removed legacy options/members
amioption.newton_preeq
and `Solver::r… by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1744Added
ReturnData::cpu_time_total
to track total time spent inrunAmiciSimulation
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1743SBML import: Alternative algorithm for identifying conservation laws by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1748
Use
amici.AmiciVersionError
to indicate version mismatch by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1764
Performance:
Optional parallel computation of derivatives during model import by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1740
Sparsify jacobian by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
Speedup for models with conservation laws by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1765
Speedup conservation law computation by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1754
Exploit stoichiometric matrix in pysb import by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1761
Speedup edata construction from petab problems by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1746
Fixes:
Fixed
get_model_settings
that would to setting incorrect initial states and initial state sensitivities for models with parameter-dependent initial states by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1751Use correct tolerances for convergence check in Newton solver by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1728
Harmonized convergence checks by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1731
Made sundials’ KLU_INDEXTYPE match actual klu index type by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1733
Fixed
Model::setStateIsNonNegative
logic that would raise exceptions in cases where it shouldn’t by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1736Fixed undefined reference to dladdr by @kristianmeyerr in https://github.com/AMICI-dev/AMICI/pull/1738
Fixed HDF5 OSX intermediate group creation errors by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1741
Fixed recent cmake-based build issues due to changed sundials library directory by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1756
Updated Windows installation instructions by @paulflang in https://github.com/AMICI-dev/AMICI/pull/1763
… and other contributions by @FFroehlich, @dweindl
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.26…v0.11.27
v0.11.26 (2022-03-14)
New features:
Import of BioNetGenLanguage (BNGL) models by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1709
Added support for observable-dependent sigmas by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1692
Added support for pysb local functions by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1666
Added experimental support for conservation laws for non-constant species to SBML import: conservation laws for non-constant species by @stephanmg, @dweindl in https://github.com/AMICI-dev/AMICI/pull/1669 Enable this feature by setting environment variable
AMICI_EXPERIMENTAL_SBML_NONCONST_CLS
to any valueAllow using states eliminated by conservation laws to be used in root functions by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1677
Added support for parameter-dependent conservation laws by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1678
Added optional caching for symbolic simplifications in ODE export by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1672
Added CLI option
--no-sensitivities
toamici_import_petab
by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1688
Fixes:
SBML import: Raise in case of nested observables by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1690
Sympy 1.10 compatibility by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1694
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.25…v0.11.26
v0.11.25 (2022-02-09)
Fixed a bug where
Model::setStateIsNonNegative(Model::getStateIsNonNegative())
would raise an exception in case conservation laws were enabled - by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1648Fixed a bug where
Model::setStateIsNonNegative
would be ignored in certain model expressions - by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1650Fixed a bug where special function parsing inside
min()
andmax()
would not be parsed correctly - by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1655Fixed a numpy dependency issues for Mac+ARM systems - by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1657
Fixed convergence check in Newton method - by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/1663
Add
AMICI_CXX_OPTIONS
to pass libamici-specific compiler options during CMake-based builds - by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1664Fixed various warnings and updated documentation - by @dweindl
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.24…v0.11.25
v0.11.24 (2022-02-01)
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 https://github.com/AMICI-dev/AMICI/pull/1637Dropped Python3.7 support by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1635
Include header files in CMake targets for better IDE integration by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1639
Fixes:
Fixed an issue in PEtab import where all-integer parameters would previously result in a TypeError by @stephanmg in https://github.com/AMICI-dev/AMICI/pull/1634
Fixed tempdir deletion issues for test suite on Windows by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1636
Added functions to provide state IDs/names for x_solver by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1638
Fixed docs on RTD by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1643
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.23…v0.11.24
v0.11.23 (2022-01-11)
Features:
Added overload for Model::setParameterScale with vector
by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1614 Removed assert_fun argument from gradient checking, improve output by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1609
Added get_expressions_as_dataframe by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1621
Added
id
field to ExpData and ReturnData by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1622Included condition id in dataframes by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1623
Fixes:
C++: Fixed SUNMatrixWrapper ctor for size 0 matrices by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1608
Python: Handle TemporaryDirectory cleanup failures on Windows by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1617
Python: pysb.Model.initial_conditions throws a DeprecationWarning by @PaulJonasJost in https://github.com/AMICI-dev/AMICI/pull/1620
Fixed wrong array size in warnings by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1624
NOTE: AMICI 0.11.23 requires numpy<1.22.0
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.22…v0.11.23
v0.11.22 (2021-12-02)
Require sympy>=1.9,pysb>=1.13.1 by @FFroehlich, @dweindl in https://github.com/AMICI-dev/AMICI/pull/1599
Fixed sympy deprecation warning by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1600
Updated Windows installation instructions for Python>=3.8 by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1597
Fixed plot labels by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1598
Full Changelog: https://github.com/AMICI-dev/AMICI/compare/v0.11.21…v0.11.22
v0.11.21 (2021-11-21)
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)
v0.11.20 (2021-11-12)
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)
v0.11.19 (2021-10-13)
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
v0.11.18 (2021-07-12)
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)
v0.11.17 (2021-05-30)
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:
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)
v0.11.16 (2021-04-13)
Fixes:
Fixed serialization bug (#1490)
New:
Construction of condition specific plist for parameter mappings (#1487, #1488)
Add support for error residuals (#1489)
v0.11.15 (2021-03-31)
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
v0.11.14 (2021-03-16)
New features:
Python 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)
Micro-optimize SUNMatrixWrapper::transpose (#1439)
Remove constant triggers from roots in Heaviside (#1440)
v0.11.13 (2021-02-20)
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
…
v0.11.12 (2021-01-26)
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)
v0.11.11 (2020-12-15)
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
v0.11.10 (2020-11-30)
Bugfix release that restores compatibility with sympy 1.7
v0.11.9 (2020-11-29)
Python
General improvements to SBML import (#1312, #1316, #1315, #1322 , #1324 #1333, #1329)
Small bugfixes and improvements (#1321 )
Improve derivative computation for instances of
power
(#1320 )
C++
Fix FIM and residual computation for models with parameter dependent sigma. (#1338)
Disable chi2/residual/FIM computation for non-gaussian objective functions. (#1338)
Bugfix for integration failure during adjoint solve (#1327)
Doc
Update references (#1331, #1336)
CI
Update OpenBLAS for windows (#1334)
v0.11.8 (2020-10-21)
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)
v0.11.7 (2020-09-22)
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)
v0.11.6 (2020-08-20)
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)
v0.11.5 (2020-08-07)
General
Move repo to new organization (#1193)
Update Bibliography
Python
Fix bug for energyPySB models (#1191)
CI
Fix release deployment (#1189)
v0.11.4 (2020-08-06)
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)
v0.11.3 (2020-08-06)
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)
v0.11.2 (2020-07-17)
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)
v0.11.1 (2020-06-05)
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)
v0.11.0 (2020-05-10)
Python:
Implement support for variable compartments (#1036)
Better handling of constant species (#1047)
Better handling of C++ enums, this makes
amici.SensitivityMethod_forward
available asamici.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)
v0.10.21 (2020-04-04)
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)
v0.10.20 (2020-03-18)
Fixed (re)initialization of sensitivities if ExpData::fixedParametersPreequilibration is set (#994)
Fixed sensitivities for parameters in sigma expressions for Python/SBML in case provided expression was not just a single parameter ID
Enable parallel compilation of model files from Python (#997) based on AMICI_PARALLEL_COMPILE enviroment variable
Fixed computation of log-likelihood for log10-normal distributed noise
Added
reinitializeFixedParameterInitialStates
to ExpData (#1000) (breaking change: overrides settings inamici::Model
)Python model import now verifies that chosen model name is a valid identifier (Closes #928)
Made w available in ReturnData (Closes #990) (#992)
Fixed setting of log level when passing boolean values to verbose (#991)
Documentation now on ReadTheDocs https://amici.readthedocs.io/en/
Use proper state/observable names in plotting functions (#979)
PEtab support:
Adapt to most recent PEtab (0.1.5)
Extended support for import of PEtab models
Added support for computing cost function based on PEtab problem
Implemented handling of species in condition table
petab_import.import_model now provides reproducible parameter list (Closes #976)
Fix python import error in import_petab_problem: Add absolute paths to python path, invalidate caches and reload (#970)
Added example notebook
CI: PEtab test suite integrated in CI workflow
Added AMICI dockerfile and image deployment to dockerhub (#948)
Removed mention of ‘mex’ in warning/error ids (#968)
More informative errors on SWIG interface import failures (#959)
v0.10.19 (2020-02-13)
Python:
Fix logo display on pypi
Fix deadlocks in multithreaded python environments when using openMP parallelization
Matlab:
Fix compilation errors due to switch to C++14
v0.10.18 (2020-02-11)
General:
AMICI now comes with a logo
implement getName function for models
Updated documentation / examples
Python:
Enable MSVC compilation of Python extensions (#847)
Always recompile clibs and extensions (Closes #700)
Extended PEtab support (Running
enable multithreading in swig (#938)
Fixes pysb (#902) (#907)
C++
Build optimized AMICI and sundials by default (Closes #934)
Matlab:
Fix(matlab) Compile CalcMD5 on demand (Fixes #914)
Don’t pass empty include strings to mex
Fix Matlab compilation error if AMICI or model path contains blanks
CI:
Running additional test models
… and various minor fixes/updates
v0.10.17 (2020-01-15)
added python 3.8 support, dropped python 3.6 support (#898)
Added logging functionality (#900)
Fixes PySB import (#879, #902)
Fixes symbolic processing (#899)
Improved build scripts (#894,
Improved petab support (#886, #888, #891)
CI related fixes (#865, #896)
v0.10.16 (2019-12-11)
Sparsify dwdp to reduce computation time for adjoints (#858)
Fix(matlab) update example name example_dae_events->example_calvetti (Closes #866)
Fix nullptr deferencing for simulations with events when no measurements are provided (Fixes #866)
Fix accessing empty vector during adjoint state event update (Closes #866)
Fix pysb_import (fixes #878)
v0.10.15 (2019-12-03)
Bugfix release due to incorrect sensitivities w.r.t. sigmas introduced in 0.10.14.
No other changes.
v0.10.14 (2019-12-02)
NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.
Python:
Don’t require use of ModelPtr.get to call ExpData(Model)
Fix import in generated model Python package
Setup AMICI standalone scripts as setuptools entrypoints
Simplify symbolic sensitivity expressions during Python SBML import Fixes Infs in the Jacobian when using Hill-functions with states of 0.0.
Extended Newton solver #848
The changes that allow performing Newton tests from the paper:
G. T. Lines, Ł. Paszkowski, L. Schmiester, D. Weindl, P. Stapor, and J. Hasenauer. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks. accepted for Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Valencia, Spain, October 2019.Use SWIG>=4.0 on travis to include PyDoc in sdist / pypi package (#841)
Fix choice of likelihood formula; failed if observable names were not equal to observable IDs
Fix(sbml-import) Compartment IDs in right-hand side of Rules are not replaced and lead to undefined identifiers in c++ files
Fix invalid logging level
Speed up sympy simplification (#871)
C++:
Performance: Avoid unnecessary repeated function calls for SUNMatrixWrapper dimensions
Add AmiciApplication class as context for handling so far global settings. This allows for example setting custom logging functions for concurrent AMICI runs, e.g. in multi-thread applications (Closes #576).
Misc:
Setup performance test on github actions (#853)
Update documentation and FAQ for CBLAS requirement and others
Update reference list
v0.10.13 (2019-10-09)
BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720)
Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
Compute initial state for Model::getInitialStates if not already set (Fixes #818)
Make swig generate pydoc comments from doxygen comments #830 (Closes #745) to provide Python docstrings for C++ wrapper functions
feature(cmake) Add option to disable compiler optimizations for wrapfunctions.cpp (Fixes #828) (#829)
Change SBML test suite to pytest to allow for parallel test execution… (#824)
Fix(cmake): -E option is not available in all sed versions. Neither is the equivalent -r. Use –regexp-extended instead (Closes #826)
Refactor(python) Move PEtab import code from command line script… (#825)
Fix(core) Fix regular expressions for intel compiler (Closes #754) (#822)
Update workflow figure to include PySB (Closes #799)
Fix compiler warnings
v0.10.12 (2019-09-28)
Fix handling of species specified in PEtab condition table (#813)
Fix some Visual C++ issues, update cppcheck handling, cleanup (VisualC++ still not fully supported)
Minor fixups (#801)
Create SBML test suite result files for upload to http://sbml.org/Facilities/Database/ (#798)
v0.10.11 (2019-08-31)
Fixed setting initial conditions for preequilibration (#784)
Fixed species->parameter conversion during PEtab import (#782)
Set correct Matlab include directories in CMake (#793)
Extended and updated documentation (#785, #787)
Fix various SBML import issues
Run SBML test suite using github actions instead of travisCI (#789)
v0.10.10 (2019-08-07)
Simplify/fix AMICI installation
If available use environment modules to detect dependencies
Add SWIG installation script
Update list of publication
Update documentation
Update doc for SWIG build and custom SWIG location.
Add AMICI interface overview / workflow figure and show in README
Document environment variables for model/core compilation (Closes #737)
Added handling of abs function, since there seem to be problems with case sensitivity (#713) Closes #770
Detaills:
* cmake: Use package_ROOT environment variables
* fix(cmake) Fix finding version.txt
* cmake: Auto-detect loaded MKL environment module
* cmake: Use new FindPython3 modules where possible
* fix(python) Restore python3.6 compatibility
* Inside venv, use pip instead of pip3 which should point to the correct version
* fix(python) Workaround for missing ensurepip during venv creation [ci skip]
* feature(python) Use MKL from environment modules to provide cblas
* fix(python) Fix define_macros not being passed to setuptools for Extension
* fix(python) Fix define_macros not being passed to setuptools for clibs
* Do not always add ‘cblas’ library since users may want to override that by a cblas-compatible library with a different name (closes #736)
* Update HDF5 path hints; use shared library if static is not available.
* Check for HDF5_BASE from environment module
* Fix system-dependent sundials library directory (Fixes #749) (#750)
* Handle OSTYPE==linux in scripts/buildBNGL.sh (Fixes #751)
* Add SWIG download and build script
* Improve finding swig executable and allow user override via SWIG environment variable
* Provide installation hints if no SWIG found (Closes #724)
* Allow overriding cmake executable with environment variables in build scripts (Closes #738)
v0.10.9 (2019-07-24)
Fixup for missing version bump in v0.10.8 release. No code changes compared to v0.10.8.
v0.10.8 (2019-07-24)
Changes in this release:
All:
Updated / extended documentation
Fix reuse of
Solver
instances (#541)
C++:
Check for correct AMICI version for model in CMake
Add reporting of computation times (#699)
Python:
Fix manifest file (#698)
Fix initial amounts/concentrations in SBML import
… and various other minor fixes/improvements
v0.10.7 (2019-05-01)
Python
fix unset noise distribution when automatically generating observables in case None are passed (#691)
v0.10.6 (2019-04-19)
C++
Add SuperLUMT support (#681)
Sparsified dJydy (#686)
Enabled support of impulse-free events for DAE models (#687) - thanks to Sebastien Sten for providing a testcase for this
Python
Enabled support for piecewise functions in SBML import (#662)
Fix numeric type when constructing ExpData from Dataframes (#690)
Fix dynamic override in PETab
v0.10.5 (2019-04-08)
Bugfix release
Doc
Update documentation of Windows installation
C++
Fix missing source files in CMakeLists.txt (#658)
Set CMake policies to prevent warnings (Closes #676) (#677)
Start using gsl::span instead of raw pointers (#393) (#678)
Python
PySB parsing fix (#669)
Fix failure to propagate BLAS_LIBS contents (#665)
Require setuptools at setup (#673)
Updated PEtab import to allow for different noise models
v0.10.4 (2019-03-21)
Features / improvements:
Implement ReturnData and ExpData wrappers as more efficient views (#657)
Add list of references using AMICI (#659)
Custom llh (normal/laplace, lin/log/log10) (#656)
Bugfixes:
Speedup and fix travis build
v0.10.3 (2019-03-13)
Features / improvements:
adds the option for early termination on integration failures for runAmiciSimulations
improve runtime of
SUNMatrixWrapper::mutliply
expose finite difference routines in public API
enable parallel compilation of clib source files
Bugfixes:
fixed symbolic processing for unreleased pysb features
v0.10.2 (2019-03-07)
Features / improvements:
extended
ExpData
interface to allow for condition specific parameters, parameter scales, parameter lists, initial conditions and initial condition sensitivities.
Bugfixes:
fixed output values of
ReturnData::x_ss
andReturnData::sx_ss
v0.10.1 (2019-03-04)
travis-ci.com migration
fix problem with has{variable} functions
allow to import sbml model from string, not only file
v0.10.0 (2019-03-01)
Features / improvements:
updated sundials to 4.1.0
updated SuiteSparse to 5.4.0
added generic implementations for symbolic expressions that were sparse matrix vector products
Bugfixes:
fixed return value of
rz
when no data is provided.
v0.9.5 (2019-02-26)
Features / improvements:
allow python installations without compilation of c++ extension
improvements to ExpData <-> pandas.DataFrame interface
allow generation of matlab models from python
implement CLI interface for PEtab
improve computation time for conservation laws from pysb import
Bugfixes:
Fix sign in undamped Newton step.
Maintenance:
use newer CI images
v0.9.4 (2019-02-11)
Minor fixes only:
fix(core) Get solver diagnostics for first(last) timepoint (#588) (Closes #586)
fix(ci) Fix autodeploy (Closes #589)
v0.9.3 (2019-02-07)
CRITICAL FIXES
fix(python) fix symbolic computations for adjoint (#583)
Features
feature(python) Check for matching AMICI versions when importing model (Closes #556). Set exact AMICI version as model package requirement.
feature(core) Add option to rethrow AMICI exception (Closes #552)
feature(python) Redirect C/C++ output in stdout is redirected (e.g. in ipython notebooks) (Closes #456)
Minor fixes
fix(python) Fix doc and rename sys_pipes to something more meaningful
fix(ci) Fix premature exit of scripts/runNotebook.sh
fix(deploy) Update pyenv shims to find twine
v0.9.2 (2019-01-30)
Bugfixes:
fixes a critical bug in the newton solver
fixes multiple bugs in sbml import for degenerate models, empty stoichiometry assignments and conversion factors
improved error messages for sbml import
#560
#557
#559
v0.9.1 (2019-01-21)
Features / improvements:
make pure steadystate results available as
rdata['x_ss']
andrdata['sx_ss']
add option to specify integration tolerances for the adjoint problem via
atolB
andrtolB
Bugfixes:
improved conservation law identification to also account for constant species.
fixed a bug where simulation results were written into results of the second newton solver attempt
fixed an openMP related warning
Maintenance:
attempt to fix automatic deploy to pypi via travis
v0.9.0 (2019-01-18)
Features / improvements:
Allow computation and application of conservation laws for pysb importet models. This enables use of NewtonSolver for preequilibration for models where it was previously not possible.
Use
klu_refactor
in the sparse Newton solver instead of always usingklu_factor
and only perform symbolic factorization once (#421)Allow more detailed finiteness checks (#514)
Bugfixes:
#491
Maintenance:
Several improvements to travis log sizes and folding
Use default copy constructor for Model by implementing class wrappers for sundials matrix types (#516)
Reenable run of SBML testsuite
v0.8.2 (2019-01-07)
Features / improvements:
Speedup symbolic processing for ODE generation in python
Bugfixes:
Fix(python) Add missing deepcopy (introduced in 6847ba675f2088854db583199b8754aaa6e01576)
Fix(core) Prevent parameter scaling length mismatch (#488)
Fix(python) Set distutils dependency to current version to fix </usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: ‘long_description_content_type’>
fix(python) add symlink to version.txt to be included in package
Backwards-compatibility:
Replace ‘newline’ by literal to restore <R2016b compatibility (Fixes #493)
Maintenance:
Remove obsolete swig library build via cmake and related file copying
Provide issue template for bug reports
Providing valid SBML document to import is not optional anymore
Update documentation and tests
Add python version check and raise required version to 3.6 to prevent cryptic error messages when encountering f-strings
v0.8.1 (2018-11-25)
[all] critical Fix long standing bugs in solving steadystate problems (including preequilibration) (#471)
[all] Fix AmiVector constructor from std::vector (#471)
[python] Reenable Solver and Model copy constructors
Update documentation
v0.8.0 (2018-11-25)
replaced symengine by sympy for symbolic processing in python which fixes several critical bugs that were due to bugs in symengine (#467)
v0.7.13 (2018-11-18)
fixes a critical bug in objective function computation for models compiled using
sbml2amici
andpysb2amici
that was introduced in v0.7.12fixes a critical bug in sensitivity computation when
model.reinitializeFixedParameterInitialStates
was set to truereadds the python interface to the ExpData copy constructor that was inadvertently removed in 0.7.12 and streamlines the respective convenience wrapper to provide access to the full range of constructors.
v0.7.12 (2018-11-17)
fixed a critical bug in
amici.constructEdataFromDataFrame
enabled multithreaded simulation of multiple experiments (requires compilation with openMP)
modularized sbml import and added pysb import
v0.7.11 (2018-10-15)
[python] Added numpy and python wrappers that provide a more user friendly python API
[python] Enable import of SBML models with non-float assignment rules
[python] Enable handling of exceptions in python
[python] Enable nativ python access to std::vector data-structures
[core] Provide an API for more fine-grained control over sensitivity tolerances and steady-state tolerances
[core] Provide an API to specify non-negative state variables (this feature is still preliminary)
v0.7.10 (2018-08-29)
Fixed python SBML import
log()
issues (#412)
v0.7.9 (2018-08-24)
fixes MATLAB compilation of models
adds option to perform steady state sensitivity analysis via FSA
condition dependent intitial conditions are now newly set after preequilibration is done
v0.7.8 (2018-08-19)
bugfixes for the ExpData interface
created build configuration that enables debugging of c++ extensions on os x
fixed python sbml import when stoichiometry is empty
v0.7.7 (2018-08-17)
Fixes a couple of bugs just introduced in v0.7.6
v0.7.6 (2018-08-13)
Important: Use AMICI v0.7.7 due to https://github.com/ICB-DCM/AMICI/pull/403/commits/3a495d3db2fdbba70c2b0d52a3d4655c33c817a2
Bug fixes:
Python import: Fix log10 issues in observables (#382)
Matlab: Fix broken model compilation (#392)
Fixed simulation for models without observables (#390)
Fixed potential matlab memory leaks (#392)
Breaking C++ API changes:
Revised ExpData interface (#388)
v0.7.5 (2018-07-30)
Features/enhancements:
Add computation of residuals, residuals sensitivity, Fisher information matrix (#223)
More efficient conversion of std::vector to numpy ndarray (#375)
Allow specifying timepoints in ExpData (#370)
Minor fixes:
Condition parameters in ExpData now only temporarily override Model parameters (#371)
Ensure non-negative states for Newton solver (#378)
v0.7.4 (2018-07-27)
Features/enhancements:
Check SBML model validity (#343)
Allow per-parameter setting of amioptions::pscale from matlab interface (#350)
Documentation
Major fixes:
Don’t compile main.cpp into python model module which broke modules if amici was compiled without libhdf5 (#363)
Minor fixes:
Fix compiler warnings (#353)
Plotting, SBML example mode, …
v0.7.3 (2018-07-13)
Features:
Added symbol names to python-wrapped models and make available via Model.getParameterNames(), model.getStateNames(), …
Extended Python interface example
Python package available via pypi: https://pypi.org/project/amici/0.7.3/
v0.7.2 (2018-07-03)
Features:
Python package: more flexible HDF5 library localization
Extended CI: python tests, preequilibration tests, run in venv
Major bugfixes:
Fix python sbml model import / compilation error (undefined function)
Fix model preequilibration
Minor fixes:
Various fixes for mingw compilation of python source distribution
Cmake compatibility with < 3.8 restored
v0.7.1 (2018-06-12)
Features:
Allow specifying sigma-parameters from Python interface
Major bugfixes:
Fix dsigma_y/dp and downstream sensitivity errors
v0.7.0 (2018-06-09)
Major revision of documentation
Improved Python interface
More comprehensive Python interface example
Fixed sensitivity computation in Python-generated models
Various other bug fixes
WARNING:
For models with sigma-parameters and dsigma_y/dp != 0, dsigma_y/dp was computed incorrectly. This propagates to all dependent sensitivities. This applies also to some older releases and has been fixed in v0.7.1.
v0.6.0 (2018-05-22)
Implement experimental support for python via swig. Python interface is now usable, but API will still receive some updates in the future.
WARNING:
There is a bug in sensitivity computation for Python-generated models
Matlab C++ compilation will fail due to undefined M_PI -> Please use v0.7.0
v0.5.0 (2018-03-15)
Main new features are:
Reimplemented support for DAE equations
Added newton solver for steady state calculation and preequilibration
Better caching for recompilation of models
Blas support to allow compilation of large models with many observables
Improved SBML support
Added c++ interface
Added support for second order adjoint computation
Rewrote large parts of the code as proper c++11 code to allow easier code maintanance
Substantially extended testing in continuous integration to assure code quality
v0.4.0 (2017-05-15)
First citable version of AMICI (via zenodo integration).
Better support for standalone compilation
Improved SBML import scripts
General Code Cleanup
v0.3.0 (2016-09-05)
This update comes with many improvements, bug fixes and several new features. Most notably:
AMICI should now run on older versions of MATLAB (back to R2014a)
AMICI now compiles using older versions of Visual Studio
AMICI now also supports second order adjoint sensitivities (full (via the o2flag = 1 and as a vector product via o2flag = 2)
AMICI now supports more SBML, SBML v2 and rate rules
0.2.1 (2016-05-09)
Bugfix release. This release also includes some changes that should improve the performance on the new R2016a release of MATLAB.
v0.2 (2016-03-17)
This update comes with many improvements to the computation time for both compilation and simulation. Moreover several new features were included:
Hessian Vector products for second order forward sensitivities
Correct treatment of parameter/state dependent discontinuities for both forward and adjoint sensitivities
v0.1 (2015-11-05)
This is the initial release of the toolbox