Merge pull request #949 from ICB-DCM/release_0.10.18

Release 0.10.18

General:
* AMICI now comes with a logo
* implement getName function for models
* Updated documentation / examples

Python:
* Enable MSVC compilation of Python extensions (#847)
* Always recompile clibs and extensions (Closes #700)
* Extended PEtab support (Running
* enable multithreading in swig (#938)
* Fixes pysb (#902) (#907)

C++
* Build optimized AMICI and sundials by default (Closes #934)

Matlab:
* Fix(matlab) Compile CalcMD5 on demand (Fixes #914)
* Don't pass empty include strings to mex
* Fix Matlab compilation error if AMICI or model path contains blanks

CI:
* Running additional test models

... and various minor fixes/updates

.github/workflows/deploy_sdist.yml

@@ -0,0 +1,31 @@
+name: Deploy Python source distribution
+on: push
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    - name: apt
+      run: |
+        sudo apt-get install -y swig3.0 \
+          && sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+    - name: pip
+      run: |
+        pip3 install --upgrade --user wheel \
+          && pip3 install --upgrade --user setuptools
+
+    - name: Create AMICI sdist
+      run: |
+        cd python/sdist && /usr/bin/python3 setup.py sdist
+
+    - name: Archive sdist
+      uses: actions/upload-artifact@v1
+      with:
+        name: sdist
+        path: python/sdist/dist

.github/workflows/test-benchmark-collection-models.yml

@@ -0,0 +1,53 @@
+name: Benchmark collection
+on:
+  push:
+    branches:
+      - develop
+      - master
+
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    # install dependencies
+    - name: apt
+      run: |
+        sudo apt-get install -y swig3.0 libatlas-base-dev \
+          && sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+    - name: pip
+      run: |
+        pip3 install --upgrade --user wheel \
+          && pip3 install --upgrade --user setuptools
+    - run: pip3 install shyaml petab>=0.1.1
+    - run: |
+        echo ::add-path::${HOME}/.local/bin/
+        echo ::add-path::${GITHUB_WORKSPACE}/tests/performance/
+    # install AMICI
+    - name: Create AMICI sdist
+      run: |
+        cd python/sdist \
+          && check_time.sh create_sdist /usr/bin/python3 setup.py sdist
+    - name: Install AMICI sdist
+      run: |
+        AMICI_PARALLEL_COMPILE=2 check_time.sh \
+            install_sdist pip3 install -v --user \
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
+
+    # retrieve test models
+    - name: Download and test benchmark collection
+      # TODO do something more efficient than cloning this big repo
+      run: |
+        git clone --depth 1 https://github.com/LeonardSchmiester/Benchmark-Models.git \
+          && cd Benchmark-Models && git checkout hackathon && cd .. \
+          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models/hackathon_contributions_new_data_format/" \
+          && tests/benchmark-models/test_benchmark_collection.sh

.github/workflows/test-large-model.yml

@@ -4,7 +4,7 @@ on:
     branches:
       - develop
       - master
-      - fix_896_perftestfiles
+      - fix_945
 
   pull_request:
     branches:
@@ -52,12 +52,10 @@ jobs:
       run: |
         cd CS_Signalling_ERBB_RAS_AKT \
           && check_time.sh \
-          petab_import amici_import_petab.py -v \
+          petab_import amici_import_petab -v \
             -n 'CS_Signalling_ERBB_RAS_AKT_petab' \
-            -s 'FroehlichKes2018/PEtab/CS_Signalling_ERBB_RAS_AKT_petab.xml' \
-            -c 'FroehlichKes2018/PEtab/conditions_petab.tsv' \
-            -m 'FroehlichKes2018/PEtab/measurements_petab.tsv' \
-            -p 'FroehlichKes2018/PEtab/parameters_petab.tsv' --no-compile
+            -y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
+            --no-compile
 
     # install model package
     - name: Install test model

.gitignore

@@ -131,6 +131,7 @@ tests/sbml-test-suite/
 tests/sedml-test-suite/
 */sbml-semantic-test-cases/*
 tests/SBMLTestModels/
+tests/benchmark-models/test_bmc
 /python/test/amici-SBMLTest*/
 
 python/examples/example_steadystate/model_steadystate_scaled/*
@@ -154,10 +155,13 @@ AMICI_guide.pdf
 ThirdParty/bionetgen.tar.gz
 ThirdParty/BioNetGen-*
 ThirdParty/cpputest-master*
+ThirdParty/doxygen/*
 ThirdParty/mtocpp-master*
 ThirdParty/sundials/build/*
 ThirdParty/SuiteSparse/lib/*
 ThirdParty/SuiteSparse/share/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz
 ThirdParty/swig-*
+
+_untracked/

.travis.yml

@@ -131,6 +131,33 @@ matrix:
         on:
           branch: master
 
+    - os: windows
+      # language python currently not supported on Windows
+      language: cpp
+      compiler: msvc
+      git:
+        # clone after enabled symlinks below
+        clone: false
+      env: PATH=/c/Python37:/c/Python37/Scripts:$PATH
+      before_install:
+        - export -f travis_fold travis_nanoseconds travis_time_start travis_time_finish
+        # allow PowerShell to run scripts
+        - powershell -Command Set-ExecutionPolicy Unrestricted -Force
+        # Enable Windows developer mode to support symlinks
+        - powershell -Command New-ItemProperty -Path "HKLM:\SOFTWARE\Microsoft\Windows\CurrentVersion\AppModelUnlock" -Name AllowDevelopmentWithoutDevLicense -Value 1  -PropertyType DWord
+        # stick to python 3.7 until there is a 3.8 wheel for windows
+        # as installation from sdist fails because of reasons...
+        - choco install python --version 3.7.5
+        - choco install swig
+        - python -m pip install --upgrade pip
+        - pip install --user -U numpy
+        - git clone -c core.symlinks=true https://github.com/ICB-DCM/AMICI.git && cd AMICI
+        - if [[ "$TRAVIS_PULL_REQUEST" == "false" ]]; then git checkout -qf $TRAVIS_COMMIT; elif [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then git fetch --update-head-ok origin pull/$TRAVIS_PULL_REQUEST/head:$TRAVIS_BRANCH && git checkout $TRAVIS_BRANCH; fi
+        # run BLAS installation script
+        - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then powershell -File 'C:\Users\travis\build\AMICI\scripts\installOpenBLAS.ps1';export BLAS_LIBS BLAS_CFLAGS; fi
+        # define Windows environment variables in BLAS because PowerShell definition didn't do the trick
+        - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then export BLAS_LIBS='/LIBPATH:C:\\BLAS\\OpenBLAS-0.3.6-x64\\lib libopenblas.lib' BLAS_CFLAGS='/IC:\\BLAS\\OpenBLAS-0.3.6-x64\\include'; fi
+
 install:
     - export BASE_DIR=`pwd`
     # Build swig4.0 (not yet available with apt) to include pydoc in source distribution for pypi
@@ -146,6 +173,8 @@ install:
     - if [[ "$CI_BUILD" == "TRUE" ]]; then ./scripts/buildAmici.sh; fi
     - if [[ "$CI_ARCHIVE" == "TRUE" ]]; then ./scripts/installAmiciArchive.sh; fi
     - if [[ "$CI_PYTHON" == "TRUE" ]]; then ./scripts/installAmiciSource.sh; fi
+    - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then cd python/sdist && python setup.py sdist; fi
+    - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then pip install $(ls -t dist/amici-*.tar.gz | head -1); fi
 
 script:
     - export -f travis_fold travis_nanoseconds travis_time_start travis_time_finish

CMakeLists.txt

@@ -18,7 +18,7 @@ project(amici)
 
 set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     # require at least gcc 4.9, otherwise regex wont work properly
     if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)

README.md

@@ -1,4 +1,8 @@
-# About AMICI
+<img src="./documentation/gfx/banner.png" height="60" align="left">
+
+## Advanced Multilanguage Interface for CVODES and IDAS
+
+## About 
 
 AMICI provides a multi-language (Python, C++, Matlab) interface for the
 [SUNDIALS](https://computing.llnl.gov/projects/sundials/) solvers
@@ -99,7 +103,13 @@ and/or
   Parameter estimation for dynamical systems with discrete events and logical
   operations. Bioinformatics, 33(7), 1049-1056.
   doi:[10.1093/bioinformatics/btw764](https://doi.org/10.1093/bioinformatics/btw764)
+
+When presenting work that employs AMICI, feel free to use one of the icons in 
+[documentation/gfx/](https://github.com/ICB-DCM/AMICI/tree/master/documentation/gfx), which are available under a [CC0](documentation/gfx/LICENSE.md) license:
 
+<p align="center">
+  <img src="./documentation/gfx/logo_text.png" height="75">
+</p>
 
 ## Status of SBML support in Python-AMICI
 

documentation/gfx/LICENSE.md

@@ -0,0 +1,121 @@
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documentation/gfx/README.md

@@ -0,0 +1 @@
+The graphics in this directory are under CC0 1.0 license. See LICENSE.md file.