Update AMICI to v0.11.23 (#369)

git subrepo clone (merge) --branch=v0.11.23 --force [email protected]:AMICI-dev/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "287364e9" upstream: origin: "[email protected]:AMICI-dev/AMICI.git" branch: "v0.11.23" commit: "287364e9" git-subrepo: version: "0.4.3" origin: "https://github.com/ingydotnet/git-subrepo" commit: "be9f02a"
ICB-DCM · Feb 22, 2022 · df2e439 · df2e439
1 parent 92e9398
commit df2e439
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diff --git a/deps/AMICI/.github/workflows/deploy_branch.yml b/deps/AMICI/.github/workflows/deploy_branch.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

diff --git a/deps/AMICI/.github/workflows/deploy_release.yml b/deps/AMICI/.github/workflows/deploy_release.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

diff --git a/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml b/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

diff --git a/deps/AMICI/.github/workflows/test_performance.yml b/deps/AMICI/.github/workflows/test_performance.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

diff --git a/deps/AMICI/.github/workflows/test_python_ver_matrix.yml b/deps/AMICI/.github/workflows/test_python_ver_matrix.yml
@@ -38,7 +38,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

diff --git a/deps/AMICI/.github/workflows/test_sbml_semantic_test_suite.yml b/deps/AMICI/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -29,7 +29,7 @@ jobs:
                 "1000-1250", "1251-1780"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 1
     - name: apt

diff --git a/deps/AMICI/.gitignore b/deps/AMICI/.gitignore
@@ -154,6 +154,7 @@ python/examples/example_presimulation/model_presimulation_re/*
 python/examples/example_constant_species/model_constant_species_reduced/*
 python/examples/example_constant_species/model_constant_species/*
 python/tests/sbml_test_models/*
+python/tests/piecewise_test/*
 
 python/sdist/amici.egg-info/*
 python/sdist/amici/version.txt

diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = v0.11.20
-	commit = e79215df0fe0418271c51487238f306c719c149b
-	parent = c665547588892bca43f54c00367a1904b7826139
+	branch = v0.11.23
+	commit = 287364e9360413e8bdfa8d3d3c6bff38ced44077
+	parent = 0f1aeda07794e0c6736ead9908cac2b46697e8e5
 	cmdver = 0.4.3
 	method = merge
diff --git a/deps/AMICI/CHANGELOG.md b/deps/AMICI/CHANGELOG.md
@@ -2,6 +2,63 @@
 
 ## v0.X Series
 
+### v0.11.23 (2022-01-11)
+
+Features:
+* Added overload for Model::setParameterScale with vector<int> 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/1622
+* Included 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: