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Release 0.10.20
Release 0.10.20 --- Merge pull request #1014 from ICB-DCM/release_0.10.20 * Fixed (re)initialization of sensitivities if ExpData::fixedParametersPreequilibration is set (#994) * Fixed sensitivities for parameters in sigma expressions for Python/SBML in case provided expression was not just a single parameter ID * Enable parallel compilation of model files from Python (#997) based on AMICI_PARALLEL_COMPILE enviroment variable * Fixed computation of log-likelihood for log10-normal distributed noise * Added `reinitializeFixedParameterInitialStates` to ExpData (#1000) (**breaking change**: overrides settings in `amici::Model`) * Python model import now verifies that chosen model name is a valid identifier (Closes #928) * Made w available in ReturnData (Closes #990) (#992) * Fixed setting of log level when passing boolean values to verbose (#991) * Documentation now on ReadTheDocs https://amici.readthedocs.io/en/ * Use proper state/observable names in plotting functions (#979) * PEtab support: * Adapt to most recent PEtab (0.1.5) * Extended support for import of PEtab models * Added support for computing cost function based on PEtab problem * Implemented handling of species in condition table * petab_import.import_model now provides reproducible parameter list (Closes #976) * Fix python import error in import_petab_problem: Add absolute paths to python path, invalidate caches and reload (#970) * Added example notebook * CI: PEtab test suite integrated in CI workflow * Added AMICI dockerfile and image deployment to dockerhub (#948) * Removed mention of 'mex' in warning/error ids (#968) * More informative errors on SWIG interface import failures (#959)
2 parents 16e3d76 + c3c4723 commit f921278

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‎.github/workflows/deploy_dockerhub.yml‎

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# https://github.com/marketplace/actions/publish-docker
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name: Deploy to dockerhub
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on: [push]
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jobs:
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build:
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name: Deploy to dockerhub
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@master
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- run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
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- name: Publish to Registry
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uses: elgohr/Publish-Docker-Github-Action@2.8
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with:
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name: dweindl/amici
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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workdir: docker/
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dockerfile: Dockerfile
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tag_names: true

‎.github/workflows/deploy_sdist.yml‎

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jobs:
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build:
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name: Deploy Python source distribution
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runs-on: ubuntu-latest
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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 apt-get update \
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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: |

‎.github/workflows/sbml-semantic-test-suite.yml‎

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jobs:
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build:
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name: SBML semantic test suite
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with:
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fetch-depth: 1
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- name: apt
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run: sudo apt-get install -y swig3.0 libatlas-base-dev && sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
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run: |
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sudo apt-get update \
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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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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh

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

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- develop
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name: Benchmark collection
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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 apt-get update \
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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: pip3 install pytest shyaml
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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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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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$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
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$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab]
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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="$(pwd)/Benchmark-Models/hackathon_contributions_new_data_format/" \
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&& tests/benchmark-models/test_benchmark_collection.sh
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git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
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&& export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
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&& AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh

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

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- fix_945
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sudo apt-get update \
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&& sudo apt-get install -y swig3.0 libatlas-base-dev \
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‎.github/workflows/test-petab-test-suite.yml‎

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name: PEtab testsuite
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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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- develop
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jobs:
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build:
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name: PEtab testsuite
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runs-on: ubuntu-latest
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env:
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ENABLE_GCOV_COVERAGE: TRUE
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steps:
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- uses: actions/checkout@master
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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 update \
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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 pytest shyaml pytest-cov
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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)[petab]
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- name: Run PEtab-related unit tests
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run: |
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pytest --cov-report=xml --cov=./ tests/testMisc.py
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# retrieve test models
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- name: Download and run petab test suite
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run: |
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git clone --depth 1 https://github.com/petab-dev/petab_test_suite \
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&& cd petab_test_suite; pip3 install -e .; cd .. \
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&& AMICI_PARALLEL_COMPILE=2 pytest -v --cov-report=xml --cov-append --cov=./ tests/petab_test_suite/
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- name: Codecov
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uses: codecov/codecov-action@v1.0.6
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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flags: python
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fail_ci_if_error: true

‎.gitignore‎

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images/*
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documentation/_build/*
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sed-ml/*
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amici_models/*
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simulate_model_*_hdf.m
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tests/petab_test_suite
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*.swp

‎.readthedocs.yml‎

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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builder: html
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configuration: documentation/conf.py
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fail_on_warning: True
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# Build documentation with MkDocs
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#mkdocs:
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# configuration: mkdocs.yml
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# Optionally build your docs in additional formats such as PDF and ePub
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formats:
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- pdf
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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: 3.7
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install:
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- requirements: documentation/rtd_requirements.txt
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build:
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image: latest

‎.travis.yml‎

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- if [[ "$CI_ARCHIVE" == "TRUE" ]]; then ./scripts/installAmiciArchive.sh; fi
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- if [[ "$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 $(ls -t dist/amici-*.tar.gz | head -1); fi
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- if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then pip install -v $(ls -t dist/amici-*.tar.gz | head -1); fi
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- if [[ "$CI_CPPUTEST" == "TRUE" ]] && [[ "$TRAVIS_OS_NAME" != "linux" ]]; then $FOLD cpputest ./scripts/run-cpputest.sh; fi
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- if [[ "$CI_DOC" == "TRUE" ]]; then $FOLD doxygen ./scripts/run-doxygen.sh; fi
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- if [[ "$CI_PYTHON" == "TRUE" ]]; then $FOLD sphinx ./scripts/run-sphinx.sh; fi
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‎README.md‎

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it is also applicable to a wider range of differential equation
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## Current build status
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<a href="https://badge.fury.io/py/amici" alt="PyPI version">
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<img src="https://badge.fury.io/py/amici.svg"></a>
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<a href="https://travis-ci.com/ICB-DCM/AMICI" alt="Build Status">
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<img src="https://travis-ci.com/ICB-DCM/AMICI.svg?branch=master"></a>
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<a href="https://codecov.io/gh/ICB-DCM/AMICI" alt="CodeCov">
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<img src="https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg"></a>
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<a href="https://www.codacy.com/app/FFroehlich/AMICI" alt="Codacy">
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<img src="https://api.codacy.com/project/badge/Grade/945235766e344a7fa36278feab915ff6"></a>
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<a href="https://zenodo.org/badge/latestdoi/43677177" alt="Zenodo">
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<img src="https://zenodo.org/badge/43677177.svg"></a>
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<a href="https://amici.readthedocs.io/en/latest/?badge=latest" alt="RTD">
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<img src="https://readthedocs.org/projects/amici/badge/?version=latest"></a>
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<a href="https://bestpractices.coreinfrastructure.org/projects/3780">
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<img src="https://bestpractices.coreinfrastructure.org/projects/3780/badge"></a>
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## Features
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in [matlab/examples/](https://github.com/ICB-DCM/AMICI/tree/master/matlab/examples).
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Comprehensive documentation on installation and usage of AMICI is available
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online at [http://icb-dcm.github.io/AMICI/](http://icb-dcm.github.io/AMICI/).
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online for the [python](https://amici.readthedocs.io/en/latest/) and
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[MATLAB/C++](http://icb-dcm.github.io/AMICI/) interfaces.
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Any [contributions](http://icb-dcm.github.io/AMICI/md__c_o_n_t_r_i_b_u_t_i_n_g.html)
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to AMICI are welcome (code, bug reports, suggestions for improvements, ...).
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In addition to SBML, we also plan to implement support for the [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.org/).
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## Current build status
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<img src="https://badge.fury.io/py/amici.svg"></a>
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<a href="https://travis-ci.com/ICB-DCM/AMICI" alt="Build Status">
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<img src="https://travis-ci.com/ICB-DCM/AMICI.svg?branch=master"></a>
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<a href="https://codecov.io/gh/ICB-DCM/AMICI" alt="CodeCov">
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<img src="https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg"></a>
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<a href="https://www.codacy.com/app/FFroehlich/AMICI" alt="Codacy">
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<img src="https://api.codacy.com/project/badge/Grade/945235766e344a7fa36278feab915ff6"></a>

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