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Merge pull request #639 from ICB-DCM/develop
Minor bug fixes, new release
2 parents a322de3 + b0a1347 commit 57c8d16

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18 files changed

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‎.flake8

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E501
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# Empty method in an abstract base class
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B027
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# Disable black would make changes warning
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BLK100
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per-file-ignores =
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# Imported but unused

‎.github/workflows/ci.yml

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- main
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pull_request:
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schedule:
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# run Monday and Thursday at 03:18 UTC
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- cron: '18 15 * * MON,THU'
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# run Monday at 03:18 UTC
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- cron: '18 15 * * MON'
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jobs:
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base:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.11', '3.9']
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python-version: ['3.12', '3.11', '3.10']
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.11', '3.9']
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python-version: ['3.12']
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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uses: actions/checkout@v2
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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runs-on: macos-latest
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strategy:
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matrix:
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python-version: ['3.11', '3.9']
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python-version: ['3.12']
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.11']
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python-version: ['3.12']
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.11']
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python-version: ['3.12']
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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uses: actions/checkout@v2
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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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‎.github/workflows/deploy.yml

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on:
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release:
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types: [created]
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deploy:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.9]
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python-version: [3.12]
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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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- name: Prepare python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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‎CHANGELOG.rst

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0.12 Series
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...........
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0.12.15 (2024-10-29)
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--------------------
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General:
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* Minor improvements in the documentation
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* Minor bug fixes in dependencies
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* Minor bug fixed in general
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* Dropping support of python 3.9
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* Adding support for python 3.12
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0.12.14 (2023-11-10)
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--------------------
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Fixes (#615):
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* Fix for wrong assets path in abc-server-dash
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* Fix for wrong assets path in abc-server-dash
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General
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‎doc/conf.py

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# Add notebooks prolog to Google Colab and nbviewer
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nbsphinx_prolog = r"""
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{% set docname = 'github/icb-dcm/pyabc/blob/main/doc/' + env.doc2path(env.docname, base=None) %}
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{% set docname = 'github/icb-dcm/pyabc/blob/main/doc/' + env.doc2path(env.docname, base=None) | string %}
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.. raw:: html
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<div class="note">

‎pyabc/acceptor/__init__.py

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Acceptors handle the acceptance step.
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"""
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from .acceptor import (
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Acceptor,
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AcceptorResult,

‎pyabc/model/model.py

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.. note::
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Most likely you do not want to use this class directly, but the
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:class:`SimpleModel` instead, or even just pass a plain function
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:class:`FunctionModel` instead, or even just pass a plain function
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as model.
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Parameters
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A model which is initialized with a function which generates the samples.
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For most cases this class will be adequate.
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Note that you can also pass a plain function to the ABCSMC class, which
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then gets automatically converted to a SimpleModel.
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then gets automatically converted to a FunctionModel.
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----------
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Parameters
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----------
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maybe_model:
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Constructs a SimpleModel instance if a function is passed.
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Constructs a FunctionModel instance if a function is passed.
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If a Model instance is passed, the Model instance itself is
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returned.
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‎pyabc/petab/__init__.py

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Problem definitions in the PEtab format (https://petab.rtfd.io).
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"""
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import warnings
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from .amici import AmiciPetabImporter
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try:
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import petab
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except ImportError:
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warnings.warn(
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"PEtab import requires an installation of petab "
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"(https://github.com/PEtab-dev/PEtab). "
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"Install via `pip3 install petab`.",
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stacklevel=1,
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)

‎pyabc/petab/amici.py

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logger = logging.getLogger("ABC.PEtab")
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try:
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import petab
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import petab.C as C
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import petab.v1 as petab
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import petab.v1.C as C
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except ImportError:
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petab = C = None
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logger.error(
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for key in self.prior_scales.keys():
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par[key] = rescale(
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val=par[key],
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origin_scale=self.prior_scales,
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target_scale=self.scaled_scales,
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origin_scale=self.prior_scales[key],
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target_scale=self.scaled_scales[key],
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)
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# simulate model

‎pyabc/petab/base.py

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logger = logging.getLogger("ABC.PEtab")
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try:
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import petab
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import petab.C as C
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import petab.v1 as petab
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import petab.v1.C as C
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except ImportError:
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petab = C = None
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logger.error(

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