Release 0.4.9

Merge pull request #370 from ICB-DCM/develop

Author: dweindl

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