Release 0.4.9

Merge pull request #370 from ICB-DCM/develop

README.md

@@ -16,7 +16,7 @@ optimization problems requiring up to thousands of simulations per objective
 function evaluation on high performance computing (HPC) systems.
 
 parPE offers easy integration with
-[AMICI](https://github.com/ICB-DCM/AMICI)-generated ordinary differential
+[AMICI](https://github.com/AMICI-dev/AMICI)-generated ordinary differential
 equation (ODE) models.
 
 ## Features
@@ -27,9 +27,9 @@ parPE offers the following features:
 * improved load balancing by intermingling multiple optimization runs
   (multi-start local optimization)
 * simple integration with [SBML](http://sbml.org/) models via
-  [AMICI](https://github.com/ICB-DCM/AMICI) and
+  [AMICI](https://github.com/AMICI-dev/AMICI) and
   [PEtab](https://github.com/PEtab-dev/PEtab)
-* interfaces to [Ipopt](http://www.coin-or.org/Ipopt/),
+* interfaces to [Ipopt](https://www.coin-or.org/Ipopt/),
   [Ceres](http://ceres-solver.org/),
   [FFSQP](https://www.isr.umd.edu/news/news_story.php?id=4088) and
   [SUMSL (CALGO/TOMS 611)](http://www.netlib.org/toms/index.html) optimizers
@@ -41,7 +41,7 @@ parPE offers the following features:
 
 Although various modules of parPE can be used independently, the most
 meaningful and convenient use case is parameter optimization for an SBML model
-specified in the [PEtab](https://github.com/ICB-DCM/PEtab) format. This is
+specified in the [PEtab](https://github.com/PEtab-dev/PEtab) format. This is
 described in [doc/petab_model_import.md](doc/petab_model_import.md).
 
 ## Dependencies
@@ -58,7 +58,7 @@ For full functionality, parPE requires the following libraries:
 * [Boost](https://www.boost.org/) (serialization, thread)
 * HDF5 (>= 1.10)
 * CBLAS compatible BLAS (libcblas, Intel MKL, ...)
-* [AMICI](https://github.com/ICB-DCM/AMICI) (included in this repository)
+* [AMICI](https://github.com/AMICI-dev/AMICI) (included in this repository)
   (uses SuiteSparse, Sundials)
 * C++17 compiler
 * Python >= 3.7, including header files
@@ -136,11 +136,10 @@ parPE is being used or has been used in the following projects:
   Bioinformatics, btz581, [doi:10.1093/bioinformatics/btz581](https://doi.org/10.1093/bioinformatics/btz581)
   (preprint: [doi:10.1101/579045](https://www.biorxiv.org/content/10.1101/579045v1)).
 
-- Paul Stapor, Leonard Schmiester, Christoph Wierling, Bodo Lange,
-  Daniel Weindl, and Jan Hasenauer. 2019.
-  *Mini-Batch Optimization Enables Training of Ode Models on Large-Scale Datasets.*
-  bioRxiv. Cold Spring Harbor Laboratory.
-  preprint: [doi:10.1101/859884](https://doi.org/10.1101/859884).
+- Stapor, P., Schmiester, L., Wierling, C. et al. *Mini-batch optimization*
+  *enables training of ODE models on large-scale datasets*. Nat Commun 13, 34
+  (2022). [doi:10.1038/s41467-021-27374-6](https://doi.org/10.1038/s41467-021-27374-6)
+  (preprint: [doi:10.1101/859884](https://doi.org/10.1101/859884)).
 
 - [CanPathPro](http://canpathpro.eu/)
 
@@ -155,4 +154,4 @@ parPE has been developed within research projects receiving external funding:
 
 * Computer resources for testing parPE have been provided among others by the 
   Gauss Centre for Supercomputing / Leibniz Supercomputing Centre under grant
-  pr62li.
+  pr62li and pn72go.

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
 

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
 

deps/AMICI/.github/workflows/test_benchmark_collection_models.yml

@@ -10,6 +10,8 @@ on:
       - master
       - develop
   workflow_dispatch:
+  schedule:
+    - cron:  '48 4 * * *'
 
 jobs:
   build:
@@ -18,7 +20,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

deps/AMICI/.github/workflows/test_doc.yml

@@ -9,6 +9,8 @@ on:
       - develop
       - master
   workflow_dispatch:
+  schedule:
+    - cron:  '48 4 * * *'
 
 jobs:
   doxygen:

deps/AMICI/.github/workflows/test_matlab.yml

@@ -14,8 +14,8 @@ jobs:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Install MATLAB
-      uses: matlab-actions/setup-matlab@v0
+      uses: matlab-actions/setup-matlab@v1
     - name: Run script
-      uses: matlab-actions/run-command@v0
+      uses: matlab-actions/run-command@v1
       with:
         command: cd matlab; installAMICI; addpath tests; testModels

deps/AMICI/.github/workflows/test_performance.yml

@@ -12,14 +12,17 @@ on:
 
   workflow_dispatch:
 
+  schedule:
+    - cron:  '48 4 * * *'
+
 jobs:
   build:
     name: Performance Test
 
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

deps/AMICI/.github/workflows/test_python_cplusplus.yml

@@ -20,7 +20,7 @@ jobs:
     - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=4.5.0.2216" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_VERSION=4.6.1.2450" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
     - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH

deps/AMICI/.github/workflows/test_python_ver_matrix.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, '3.10']
         experimental: [false]
 # Temporarily disabled because the respective jobs somehow runs infinitely
 #        include:
@@ -38,7 +38,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@master
       with:
         fetch-depth: 20
 

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

deps/AMICI/.github/workflows/test_valgrind.yml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - master
-      - feature_cpp_hierarchical_derivatives
+      - update_valgrind_supp
   pull_request:
     branches:
       - master

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

deps/AMICI/.gitrepo

@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = v0.11.19
-	commit = 4610a608d05731d245218c88015d8017f81087b5
-	parent = 45e2e41b09b125fae392a790d759e944a6f48e25
+	branch = v0.11.23
+	commit = 287364e9360413e8bdfa8d3d3c6bff38ced44077
+	parent = 0f1aeda07794e0c6736ead9908cac2b46697e8e5
 	cmdver = 0.4.3
 	method = merge

deps/AMICI/.readthedocs.yml

@@ -11,19 +11,18 @@ sphinx:
   configuration: documentation/conf.py
   fail_on_warning: True
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
 formats:
   - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
   install:
     - requirements: documentation/rtd_requirements.txt
 
 build:
-  image: latest
+  os: "ubuntu-20.04"
+  apt_packages:
+    # for custom doxygen
+    - libclang-cpp9
+    - libclang1-9
+  tools:
+    python: "3.8"

deps/AMICI/CHANGELOG.md

@@ -2,6 +2,80 @@
 
 ## 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: 
+ * Changed parameter mappings such that unassigned values have non-nan default values. This fixes erroneous evaluation of `llh` as `NaN` in some situations (#1574)
+ * Added support for Python 3.10 (#1555)
+
+Fixes:
+ * Fixed a bug when simulation start time was not transferred when copying a solver instance (#1573)
+ * Fixed a bug which led to incorrect sensitivies for models with multiple assignment rules or rate rules (#1584)
+
+Other:
+ * Update CI and documentation settings (#1569, #1527, #1572, #1575, #1579, #1580, #1589, #1581)
+ * Extend set of validated benchmark models that is checked during CI (#1571, #1577)
+ * Fixed string formatting in derivative checks (#1585)
+ * Added helper methods to save and restore model instance-only settings (#1576)
+
+
 ### v0.11.19 (2021-10-13)
 
 New: