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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
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.github/workflows/deploy_sdist.yml

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

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

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

.gitignore

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tests/sedml-test-suite/
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*/sbml-semantic-test-cases/*
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tests/SBMLTestModels/
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tests/benchmark-models/test_bmc
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/python/test/amici-SBMLTest*/
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python/examples/example_steadystate/model_steadystate_scaled/*
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ThirdParty/bionetgen.tar.gz
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ThirdParty/BioNetGen-*
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ThirdParty/cpputest-master*
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ThirdParty/doxygen/*
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ThirdParty/mtocpp-master*
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ThirdParty/sundials/build/*
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ThirdParty/SuiteSparse/lib/*
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ThirdParty/SuiteSparse/share/*
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ThirdParty/SuperLU_MT_3.1/
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ThirdParty/superlu_mt_3.1.tar.gz
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ThirdParty/swig-*
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_untracked/

.travis.yml

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

CMakeLists.txt

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set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
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set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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set(CMAKE_CXX_STANDARD 11)
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set(CMAKE_CXX_STANDARD 14)
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if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
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if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)

README.md

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

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documentation/gfx/README.md

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The graphics in this directory are under CC0 1.0 license. See LICENSE.md file.

documentation/gfx/banner.png

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