Release 0.11.26

Merge pull request #1698 from AMICI-dev/release_0.11.26

.github/workflows/test_pypi.yml

@@ -31,7 +31,11 @@ jobs:
       - name: homebrew
         run: |
           if [[ ${{ matrix.os }} == macos* ]] ; then \
-            brew install hdf5 swig gcc libomp
+            brew install [email protected] swig gcc libomp \
+               && echo "/usr/local/opt/[email protected]/bin" >> $GITHUB_PATH \
+               && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/[email protected]/lib" >> $GITHUB_ENV \
+               && echo CPPFLAGS="-I/usr/local/opt/[email protected]/include" >> $GITHUB_ENV \
+               && echo HDF5_BASE="/usr/local/opt/[email protected]/" >> $GITHUB_ENV
           fi
 
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_python_cplusplus.yml

@@ -152,7 +152,13 @@ jobs:
     # install amici dependencies
     - name: homebrew
       run: |
-        brew install hdf5 swig gcc cppcheck libomp boost
+        brew install [email protected] swig gcc cppcheck libomp boost \
+          && brew ls -v boost \
+          && brew ls -v libomp \
+          && echo "/usr/local/opt/[email protected]/bin" >> $GITHUB_PATH \
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/[email protected]/lib -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I/usr/local/opt/[email protected]/include -I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV \
+          && echo HDF5_BASE="/usr/local/opt/[email protected]/" >> $GITHUB_ENV
 
     - name: Build AMICI
       run: |

.github/workflows/test_valgrind.yml

@@ -10,7 +10,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  valgrind:
     name: Tests Valgrind
 
     # TODO: prepare image with more deps preinstalled
@@ -20,6 +20,9 @@ jobs:
       matrix:
         python-version: [ 3.8 ]
 
+    env:
+      ENABLE_AMICI_DEBUGGING: "TRUE"
+
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2

.gitignore

@@ -136,6 +136,7 @@ tests/test/*
 */tests/fricker_2010_apoptosis_amici/*
 */tests/explicit_amici/*
 */tests/fixed_initial_amici/*
+*/tests/localfunc_amici/*
 tests/cpp/writeResults.h5
 tests/cpp/writeResults.h5.bak
 tests/sbml-test-suite/*
@@ -191,6 +192,6 @@ tests/performance/CS_Signalling_ERBB_RAS_AKT/
 tests/performance/CS_Signalling_ERBB_RAS_AKT_petab/*
 coverage_SBMLSuite.xml
 Benchmark-Models-PEtab/
-
+/test_bmc/
 
 CS_Signalling_ERBB_RAS_AKT/

CHANGELOG.md

@@ -2,6 +2,37 @@
 
 ## v0.X Series
 
+### 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 value
+  * Allow 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` to `amici_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