Releases: AMICI-dev/AMICI
AMICI v0.10.14
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
AMICI v0.10.13
- 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
AMICI v0.10.12
- 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)
AMICI v0.10.11
- 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)
AMICI v0.10.10
-
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)
AMICI v0.10.9
Fixup for missing version bump in v0.10.8 release. No code changes compared to v0.10.8.
AMICI v0.10.8
Changes in this release:
All:
- Updated / extended documentation
- Fix reuse of
Solverinstances (#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
AMICI v0.10.7
Python
- fix unset noise distribution when automatically generating observables in case None are passed (#691)
