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Preparation for release 0.12.16 (#646)
* Update deploy.yml * Update deploy.yml (#643) * Update deploy.yml Upgrade actions/checkout@v2 -> actions/checkout@v4. * Update deploy.yml According to docs username must be __token__ when using API token: https://pypi.org/help/#invalid-auth * Update deploy.yml We need to generate PYP_API_TOKEN once we have access. __token__ is required, since we do authenticate with an API token and not username password combination. * Fix CI. * Enabling CI on develop branch. * Upgrade GHA cache to v4. * Try to fix R dependencies. * Try fix R dependencies for latest ubuntu. * Adding liblzma-dev. * Adding more required R (runtime) dependencies. * Fix R dependencies. * Change module import amici.petab_import -> amici.petab.petab_import * Fix tests. * Adding LD_LIBRARY path to tox.ini for manually build R. * Another try to fix dependencies. * Correcting LD_LIBRARY_PATH. * Use pyABC with amici extra. * Split up testing of external simulators. * Revert "Split up testing of external simulators." This reverts commit 5de4d6a. * Correcting tox.ini. * Updating tox.ini for base. * Fix tox.ini syntax. * Fix notebooks2. * Adding assert. * Debugging. * More debugging. * Removing debugging statement. * Try to fix PEtab unit tests. * Try to fix PEtab unit tests. * Debugging CI. * Install pyabc with amici extra. * Try to force tox to use installed amici. * More debugging. * Adding pytest to tox environment. * Adding pytest to tox environment. * Fix petab tests. * Re-installing pyabc with amici explictly in tox. * Fix petab imports. * Cleanup. * Release v0.12.16. --------- Co-authored-by: Jonas Arruda <[email protected]>
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‎.flake8

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B027
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# Disable black would make changes warning
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BLK100
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# Name is never assigned to scope
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per-file-ignores =
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# Imported but unused

‎.github/workflows/ci.yml

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push:
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branches:
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- main
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- develop
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pull_request:
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schedule:
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# run Monday at 03:18 UTC
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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path: ~/.cache
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-base
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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version: 1.7
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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path: ~/.cache
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-external
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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path: ~/.cache
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-petab
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- name: Run tests
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timeout-minutes: 20
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run: tox -e petab
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run: |
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echo "Amici installed (1):"
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pip list | grep amici
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tox -e petab -vvv
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echo "Amici installed (2):"
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pip list | grep amici
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- name: Coverage
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uses: codecov/codecov-action@v2
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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path: ~/Library/Caches/pip
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-mac
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-notebooks1
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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with:
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v4
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key: ci-${{ runner.os }}-${{ matrix.python-version }}-quality

‎.github/workflows/install_deps.sh

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# MacOS
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brew install r
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else
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# Linux
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wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo gpg --dearmor -o /usr/share/keyrings/r-project.gpg
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echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee -a /etc/apt/sources.list.d/r-project.list
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sudo apt-get update
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sudo apt-get install r-base
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# Linux (Not compatible with Ubuntu 24: no CRAN repository currently available)
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#wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo gpg --dearmor -o /usr/share/keyrings/r-project.gpg
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#echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee -a /etc/apt/sources.list.d/r-project.list
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#sudo apt-get update
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#sudo apt-get install libtiff5 r-base
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sudo apt update
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sudo apt install -y build-essential libreadline-dev libx11-dev libxt-dev libpng-dev libjpeg-dev libcairo2-dev libssl-dev libcurl4-openssl-dev libxml2-dev texinfo texlive texlive-fonts-extra screen wget
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sudo apt install -y liblzma-dev
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sudo apt install -y \
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build-essential \
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libreadline-dev \
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libx11-dev \
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libxt-dev \
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libpng-dev \
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libjpeg-dev \
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libcairo2-dev \
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libtiff-dev \
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libglib2.0-dev \
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liblzma-dev \
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libbz2-dev \
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libzstd-dev \
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libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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texinfo \
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texlive \
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texlive-fonts-extra \
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texlive-latex-extra \
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zlib1g-dev \
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gfortran \
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libpcre2-dev \
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libicu-dev \
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libboost-all-dev
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cd /tmp
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wget https://cran.r-project.org/src/base/R-4/R-4.4.0.tar.gz
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tar -xvzf R-4.4.0.tar.gz
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sudo make install
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;;
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amici)
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sudo apt-get install swig libatlas-base-dev libhdf5-serial-dev
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sudo apt-get install swig libatlas-base-dev libhdf5-serial-dev libboost-all-dev
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pip install 'pyabc[amici]'
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;;
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‎CHANGELOG.rst

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0.12 Series
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...........
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0.12.16 (2025-05-23)
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--------------------
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General:
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* Migration to PEtab v2.
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0.12.15 (2024-10-29)
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--------------------
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‎pyabc/petab/amici.py

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try:
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import amici
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from amici import petab_import as amici_petab_import
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from amici.petab_objective import LLH, RDATAS, simulate_petab
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from amici.petab import petab_import as amici_petab_import
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from amici.petab.simulations import LLH, RDATAS, simulate_petab
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amici = amici_petab_import = simulate_petab = LLH = RDATAS = None
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logger.error(

‎pyabc/version.py

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__version__ = '0.12.15'
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__version__ = '0.12.16'

‎test/petab/test_petab.py

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import os
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import sys
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import amici.petab_import
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import amici.petab.petab_import
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import cloudpickle as pickle
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import git
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import matplotlib.pyplot as plt
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if output_folder not in sys.path:
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sys.path.insert(0, output_folder)
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model = amici.petab_import.import_petab_problem(
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model = amici.petab.petab_import.import_petab_problem(
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petab_problem,
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model_output_dir=output_folder,
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generate_sensitivity_code=False,

‎test/petab/test_petab_suite.py

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import pyabc
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import amici.petab.petab_import
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import petab.v1 as petab
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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simulation_df = amici.petab.simulations.rdatas_to_measurement_df(
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‎tox.ini

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# Unit tests
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[testenv:base]
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setenv =
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LD_LIBRARY_PATH = {env:LD_LIBRARY_PATH:/usr/lib}:/usr/local/lib/R/lib
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extras = test,R,pyarrow,autograd
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passenv = HOME
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commands =
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setenv =
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LD_LIBRARY_PATH = {env:LD_LIBRARY_PATH:/usr/lib}:/usr/local/lib/R/lib
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extras = test,plotly,webserver_dash,webserver_flask
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commands =
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pytest --cov=pyabc --cov-report=xml --cov-append \
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test/visualization
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Test visualization
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[testenv:external]
68-
extras = test,R,julia,copasi
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[testenv:external-R]
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setenv =
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LD_LIBRARY_PATH = {env:LD_LIBRARY_PATH:/usr/lib}:/usr/local/lib/R/lib
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extras = test,R
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# General
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pytest --cov=pyabc --cov-report=xml --cov-append \
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test/external/test_external.py -s
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test/external/test_rpy2.py -s
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description =
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[testenv:external-other-simulators]
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extras = test,julia,copasi
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commands =
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python -c "import julia; julia.install()"
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python -m pytest --cov=pyabc --cov-report=xml --cov-append \
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[testenv:petab]
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# Petab
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python -m pytest --cov=pyabc --cov-report=xml --cov-append \
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description =
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Run notebooks
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[testenv:notebooks2]
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setenv =
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LD_LIBRARY_PATH = {env:LD_LIBRARY_PATH:/usr/lib}:/usr/local/lib/R/lib
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allowlist_externals = bash
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extras = examples,R,petab,yaml2sbml,amici,autograd
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commands =

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