git subrepo clone (merge) --branch=65ac883bd5ff0769181b0a1d1c313b4ada…

…2fbe8e --force git@github.com:dweindl/AMICI.git deps/AMICI

subrepo:
  subdir:   "deps/AMICI"
  merged:   "65ac883b"
upstream:
  origin:   "git@github.com:dweindl/AMICI.git"
  branch:   "65ac883bd5ff0769181b0a1d1c313b4ada2fbe8e"
  commit:   "65ac883b"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"

deps/AMICI/.github/workflows/test_petab_test_suite.yml

@@ -79,7 +79,7 @@ jobs:
           source ./venv/bin/activate \
             && python3 -m pip uninstall -y petab \
             && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
-            && python3 -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching \
+            && python3 -m pip install git+https://github.com/pysb/pysb@master \
             && python3 -m pip install sympy>=1.12.1
 
 

deps/AMICI/.gitrepo

@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = git@github.com:ICB-DCM/AMICI.git
-	branch = ee2e0d2189e047558c8dc1a1d8fc171446ec4203
-	commit = ee2e0d2189e047558c8dc1a1d8fc171446ec4203
-	parent = 5cdcd62f892854fa197f6513b0a520ec2c1cb0e6
+	branch = 65ac883bd5ff0769181b0a1d1c313b4ada2fbe8e
+	commit = 65ac883bd5ff0769181b0a1d1c313b4ada2fbe8e
+	parent = 741dbcf85710649fa430ba7a40c6e3864d4bf6e1
 	cmdver = 0.4.6
 	method = merge

deps/AMICI/documentation/python_installation.rst

@@ -45,7 +45,7 @@ Install the AMICI dependencies via ``apt``
    sudo apt install libhdf5-serial-dev
 
    # optionally for boost support (thread-specific CPU times, extended math functions, serialization)
-   libboost-chrono-dev libboost-math-dev libboost-serialization-dev
+   sudo apt install libboost-chrono-dev libboost-math-dev libboost-serialization-dev
 
 Install AMICI:
 

deps/AMICI/python/sdist/amici/de_model.py

@@ -2226,7 +2226,7 @@ def _get_unique_root(
 
     def _collect_heaviside_roots(
         self,
-        args: Sequence[sp.Expr],
+        args: Sequence[sp.Basic],
     ) -> list[sp.Expr]:
         """
         Recursively checks an expression for the occurrence of Heaviside
@@ -2288,7 +2288,7 @@ def _process_heavisides(
         # replace them later by the new expressions
         heavisides = []
         # run through the expression tree and get the roots
-        tmp_roots_old = self._collect_heaviside_roots(dxdt.args)
+        tmp_roots_old = self._collect_heaviside_roots((dxdt,))
         for tmp_old in unique_preserve_order(tmp_roots_old):
             # we want unique identifiers for the roots
             tmp_new = self._get_unique_root(tmp_old, roots)

deps/AMICI/python/sdist/amici/petab/util.py

@@ -71,7 +71,7 @@ def get_states_in_condition_table(
             raise NotImplementedError(
                 "Requires https://github.com/pysb/pysb/pull/570. "
                 "To use this functionality, update pysb via "
-                "`pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching`"
+                "`pip install git+https://github.com/pysb/pysb@master`"
             )
 
         # expose model components as variables so we can evaluate patterns

deps/AMICI/scripts/installAmiciSource.sh

@@ -34,7 +34,7 @@ export PYTHON_EXECUTABLE="${AMICI_PATH}/venv/bin/python"
 
 python -m pip install --upgrade pip wheel
 python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab
-python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
+python -m pip install git+https://github.com/pysb/pysb@master # for SPM with compartments
 AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
   python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis]" --no-build-isolation
 deactivate

deps/AMICI/tests/benchmark-models/test_benchmark_collection.sh

@@ -15,7 +15,7 @@ Brannmark_JBC2010
 Bruno_JExpBot2016
 Crauste_CellSystems2017
 Elowitz_Nature2000
-Fiedler_BMC2016
+Fiedler_BMCSystBiol2016
 Fujita_SciSignal2010
 Isensee_JCB2018
 Lucarelli_CellSystems2018