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Releases: AMICI-dev/AMICI

AMICI v0.11.12

26 Jan 17:07
b113544
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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

15 Dec 22:23
a5c679b
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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

30 Nov 15:11
275e599
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Bugfix release that restores compatibility with sympy 1.7

AMICI v0.11.9

29 Nov 20:01
9847fa2
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Python

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

CI

  • Update OpenBLAS for windows (#1334)

AMICI v0.11.8

21 Oct 13:38
6aa87c3
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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

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

22 Sep 23:37
d16078e
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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

CI

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

AMICI v0.11.6

20 Aug 12:41
7a1dc5e
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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

07 Aug 23:25
055b1df
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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

06 Aug 20:03
93cc940
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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

06 Aug 00:10
a4324d0
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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++

CI

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