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Merge pull request #201 from PEtab-dev/release_0.2.0
Release 0.2.0
2 parents 2ba5c52 + 9fbf14c commit 3c29fa1

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‎.flake8

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exclude =
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build
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dist
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doc
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env
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venv
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example
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tmp
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_*
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build,
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dist,
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doc,
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env,
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venv,
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example,
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tmp,
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_*,
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.tox,

‎.github/CODEOWNERS

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# see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
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# default owners
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* @PEtab-dev/libpetab-python-maintainers
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/petab/visualize/ @plakrisenko
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/tests/test_vis* @plakrisenko
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/petab/simulate.py @dilpath
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/tests/test_simulate.py @dilpath
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/petab/calculate.py @yannikschaelte
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/tests/test_calculate.py @yannikschaelte
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/doc/ @dweindl

‎.github/workflows/ci_tests.yml

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strategy:
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matrix:
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platform: [windows-latest, macos-latest, ubuntu-latest]
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python-version: ["3.8", "3.10"]
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python-version: ["3.9", "3.11"]
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runs-on: ${{ matrix.platform }}
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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@v3
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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: ${{ matrix.python-version }}
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- name: Get pip cache directory
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id: pip_cache_dir
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: Cache
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uses: actions/cache@v1
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uses: actions/cache@v3
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with:
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path: ${{ steps.pip_cache_dir.outputs.dir }}
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key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/.ci_pip_reqs.txt') }}-${{ hashFiles('**/setup.py') }}
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run: tox -e unit
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- name: Coverage
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uses: codecov/codecov-action@v1
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uses: codecov/codecov-action@v3
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml

‎.github/workflows/deploy.yml

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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@v3
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- name: Set up python
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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: 3.8
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python-version: 3.11
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip

‎.readthedocs.yaml

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configuration: doc/conf.py
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fail_on_warning: true
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build:
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os: "ubuntu-22.04"
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tools:
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python: "3.9"
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python:
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version: 3.8
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install:
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- method: pip
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path: .
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extra_requirements:
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- doc
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- vis

‎CHANGELOG.md

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# PEtab changelog
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## 0.2 series
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### 0.2.0
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Note: petab 0.2.0 requires Python>=3.9
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Features:
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* Plot measurements for t = 'inf'
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/149
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* Added validation for visualization files
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/184
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https://github.com/PEtab-dev/libpetab-python/pull/189
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* Startpoints as dict
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/188
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* Residuals plot
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/187
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https://github.com/PEtab-dev/libpetab-python/pull/191
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* add goodness of fit plot
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/192
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* Add PySBModel for handling of PySB models
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/145
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Fixes
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* Vis: Don't fail on missing simulations
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/185
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* prevent strings being parsed as nan in get_visualization_df
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/193
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* Fix get_model_for_condition
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/194
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* Simulator: rename measurement column to simulation
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by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/199
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* Fix sympy symbol name clashes
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/202
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**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.30...v0.2.0
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## 0.1 series
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### 0.1.30

‎doc/example/example_Fujita/Fujita_measurementData_t_inf.tsv

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observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId
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pS6_tot model1_data1 0 0 scaling_pS6_tot 0.01 model1_data1_pS6_tot
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pS6_tot model1_data1 0.0018563 60 scaling_pS6_tot 0.01 model1_data1_pS6_tot
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pS6_tot model1_data1 0.0033416 120 scaling_pS6_tot 0.01 model1_data1_pS6_tot
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pS6_tot model1_data1 0.012632 300 scaling_pS6_tot 0.01 model1_data1_pS6_tot
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pS6_tot model1_data1 0.078914 600 scaling_pS6_tot 0.02 model1_data1_pS6_tot
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pS6_tot model1_data1 0.25521 900 scaling_pS6_tot 0.02 model1_data1_pS6_tot
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pS6_tot model1_data1 0.44745 1800 scaling_pS6_tot 0.035 model1_data1_pS6_tot
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pS6_tot model1_data1 0.29547 inf scaling_pS6_tot 0.035 model1_data1_pS6_tot
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pS6_tot model1_data2 0 0 scaling_pS6_tot 0.01 model1_data2_pS6_tot
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pS6_tot model1_data2 0.0019654 60 scaling_pS6_tot 0.01 model1_data2_pS6_tot
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pS6_tot model1_data2 0.0021975 120 scaling_pS6_tot 0.01 model1_data2_pS6_tot
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pS6_tot model1_data2 0.020119 300 scaling_pS6_tot 0.01 model1_data2_pS6_tot
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pS6_tot model1_data2 0.22158 600 scaling_pS6_tot 0.02 model1_data2_pS6_tot
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pS6_tot model1_data2 0.52331 900 scaling_pS6_tot 0.03 model1_data2_pS6_tot
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pS6_tot model1_data2 0.85846 1800 scaling_pS6_tot 0.1 model1_data2_pS6_tot
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pS6_tot model1_data2 0.6598 inf scaling_pS6_tot 0.025 model1_data2_pS6_tot
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pS6_tot model1_data3 0 0 scaling_pS6_tot 0.01 model1_data3_pS6_tot
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pS6_tot model1_data3 0.0020839 60 scaling_pS6_tot 0.01 model1_data3_pS6_tot
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pS6_tot model1_data3 0.0047955 120 scaling_pS6_tot 0.01 model1_data3_pS6_tot
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pS6_tot model1_data3 0.047495 300 scaling_pS6_tot 0.01 model1_data3_pS6_tot
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pS6_tot model1_data3 0.39197 600 scaling_pS6_tot 0.01 model1_data3_pS6_tot
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pS6_tot model1_data3 0.68142 900 scaling_pS6_tot 0.025 model1_data3_pS6_tot
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pS6_tot model1_data3 1.0001 1800 scaling_pS6_tot 0.07 model1_data3_pS6_tot
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pS6_tot model1_data3 0.75108 inf scaling_pS6_tot 0.075 model1_data3_pS6_tot
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pS6_tot model1_data4 0 0 scaling_pS6_tot 0.01 model1_data4_pS6_tot
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pS6_tot model1_data4 0.0057189 60 scaling_pS6_tot 0.01 model1_data4_pS6_tot
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pS6_tot model1_data4 0.013126 120 scaling_pS6_tot 0.01 model1_data4_pS6_tot
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pS6_tot model1_data4 0.062408 300 scaling_pS6_tot 0.01 model1_data4_pS6_tot
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pS6_tot model1_data4 0.41154 600 scaling_pS6_tot 0.01 model1_data4_pS6_tot
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pS6_tot model1_data4 0.71428 900 scaling_pS6_tot 0.035 model1_data4_pS6_tot
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pS6_tot model1_data4 0.92784 1800 scaling_pS6_tot 0.08 model1_data4_pS6_tot
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pS6_tot model1_data4 0.55064 inf scaling_pS6_tot 0.08 model1_data4_pS6_tot
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pS6_tot model1_data5 0 0 scaling_pS6_tot 0.01 model1_data5_pS6_tot
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pS6_tot model1_data5 0.0073292 60 scaling_pS6_tot 0.01 model1_data5_pS6_tot
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pS6_tot model1_data5 0.014418 120 scaling_pS6_tot 0.01 model1_data5_pS6_tot
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pS6_tot model1_data5 0.079732 300 scaling_pS6_tot 0.01 model1_data5_pS6_tot
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pS6_tot model1_data5 0.4562 600 scaling_pS6_tot 0.01 model1_data5_pS6_tot
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pS6_tot model1_data5 0.65294 900 scaling_pS6_tot 0.02 model1_data5_pS6_tot
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pS6_tot model1_data5 0.75189 1800 scaling_pS6_tot 0.04 model1_data5_pS6_tot
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pS6_tot model1_data5 0.37446 inf scaling_pS6_tot 0.08 model1_data5_pS6_tot
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pS6_tot model1_data6 0 0 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.0086144 60 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.013062 120 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.07993 300 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.42868 600 scaling_pS6_tot 0.02 model1_data6_pS6_tot
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pS6_tot model1_data6 0.60508 900 scaling_pS6_tot 0.03 model1_data6_pS6_tot
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pS6_tot model1_data6 0.62088 1800 scaling_pS6_tot 0.035 model1_data6_pS6_tot
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pS6_tot model1_data6 0.32084 inf scaling_pS6_tot 0.07 model1_data6_pS6_tot
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pS6_tot model1_data6 0 0 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.009 60 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.01 120 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.05 300 scaling_pS6_tot 0.01 model1_data6_pS6_tot
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pS6_tot model1_data6 0.6 600 scaling_pS6_tot 0.02 model1_data6_pS6_tot
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pS6_tot model1_data6 0.4 900 scaling_pS6_tot 0.03 model1_data6_pS6_tot
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pS6_tot model1_data6 0.83 1800 scaling_pS6_tot 0.035 model1_data6_pS6_tot
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pS6_tot model1_data6 0.2 inf scaling_pS6_tot 0.07 model1_data6_pS6_tot

‎doc/example/example_Fujita/Fujita_simulatedData_t_inf.tsv

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observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters
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pS6_tot model1_data1 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data1 5.78895984805857E-05 60 scaling_pS6_tot 0.01
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pS6_tot model1_data1 0.0009531255 120 scaling_pS6_tot 0.01
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pS6_tot model1_data1 0.0185497283 300 scaling_pS6_tot 0.01
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pS6_tot model1_data1 0.0927501675 600 scaling_pS6_tot 0.02
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pS6_tot model1_data1 0.1859892615 900 scaling_pS6_tot 0.02
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pS6_tot model1_data1 0.3842285889 1800 scaling_pS6_tot 0.035
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pS6_tot model1_data1 0.3671651134 inf scaling_pS6_tot 0.035
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pS6_tot model1_data2 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data2 0.0001694707 60 scaling_pS6_tot 0.01
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pS6_tot model1_data2 0.0026563935 120 scaling_pS6_tot 0.01
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pS6_tot model1_data2 0.045833771 300 scaling_pS6_tot 0.01
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pS6_tot model1_data2 0.209607514 600 scaling_pS6_tot 0.02
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pS6_tot model1_data2 0.4007484657 900 scaling_pS6_tot 0.03
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pS6_tot model1_data2 0.7556316274 1800 scaling_pS6_tot 0.1
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pS6_tot model1_data2 0.6612775029 inf scaling_pS6_tot 0.025
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pS6_tot model1_data3 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data3 0.0005211244 60 scaling_pS6_tot 0.01
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pS6_tot model1_data3 0.007106942 120 scaling_pS6_tot 0.01
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pS6_tot model1_data3 0.0945320284 300 scaling_pS6_tot 0.01
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pS6_tot model1_data3 0.366852041 600 scaling_pS6_tot 0.01
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pS6_tot model1_data3 0.6350909024 900 scaling_pS6_tot 0.025
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pS6_tot model1_data3 0.9989387811 1800 scaling_pS6_tot 0.07
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pS6_tot model1_data3 0.7818807584 inf scaling_pS6_tot 0.075
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pS6_tot model1_data4 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data4 0.001284326 60 scaling_pS6_tot 0.01
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pS6_tot model1_data4 0.0137701475 120 scaling_pS6_tot 0.01
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pS6_tot model1_data4 0.1357831768 300 scaling_pS6_tot 0.01
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pS6_tot model1_data4 0.4317319675 600 scaling_pS6_tot 0.01
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pS6_tot model1_data4 0.6581119566 900 scaling_pS6_tot 0.035
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pS6_tot model1_data4 0.8936164338 1800 scaling_pS6_tot 0.08
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pS6_tot model1_data4 0.6665565723 inf scaling_pS6_tot 0.08
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pS6_tot model1_data5 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data5 0.0026774961 60 scaling_pS6_tot 0.01
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pS6_tot model1_data5 0.0210783997 120 scaling_pS6_tot 0.01
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pS6_tot model1_data5 0.1570157565 300 scaling_pS6_tot 0.01
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pS6_tot model1_data5 0.4117751573 600 scaling_pS6_tot 0.01
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pS6_tot model1_data5 0.5823970015 900 scaling_pS6_tot 0.02
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pS6_tot model1_data5 0.7468131737 1800 scaling_pS6_tot 0.04
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pS6_tot model1_data5 0.5504628923 inf scaling_pS6_tot 0.08
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pS6_tot model1_data6 0 0 scaling_pS6_tot 0.01
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pS6_tot model1_data6 0.0039799398 60 scaling_pS6_tot 0.01
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pS6_tot model1_data6 0.0254606658 120 scaling_pS6_tot 0.01
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pS6_tot model1_data6 0.1631478226 300 scaling_pS6_tot 0.01
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pS6_tot model1_data6 0.4009703836 600 scaling_pS6_tot 0.02
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pS6_tot model1_data6 0.5574326493 900 scaling_pS6_tot 0.03
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pS6_tot model1_data6 0.7058108511 1800 scaling_pS6_tot 0.035
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pS6_tot model1_data6 0.5194180219 inf scaling_pS6_tot 0.07

‎doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_replicates.tsv

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plotId xValues yValues yOffset yScale plotName plotTypeSimulation plotTypeData
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plot1 time pS6_tot 0 lin pS6 total LinePlot replicate

‎petab/C.py

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#: Supported plot types
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PLOT_TYPES_SIMULATION = [LINE_PLOT, BAR_PLOT, SCATTER_PLOT]
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#: Supported xScales
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X_SCALES = [LIN, LOG, LOG10]
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#: Supported yScales
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Y_SCALES = [LIN, LOG, LOG10]
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MEAN_AND_SD = 'MeanAndSD'
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#:
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SBML_FILES = 'sbml_files'
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#:
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MODEL_FILES = 'model_files'
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#:
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MODEL_LOCATION = 'location'
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#:
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MODEL_LANGUAGE = 'language'
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#:
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CONDITION_FILES = 'condition_files'
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MEASUREMENT_FILES = 'measurement_files'
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VISUALIZATION_FILES = 'visualization_files'
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MAPPING_FILES = 'mapping_files'
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EXTENSIONS = 'extensions'
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# MAPPING
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#:
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PETAB_ENTITY_ID = 'petabEntityId'
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#:
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MODEL_ENTITY_ID = 'modelEntityId'
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#:
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MAPPING_DF_REQUIRED_COLS = [PETAB_ENTITY_ID, MODEL_ENTITY_ID]
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# MORE
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#:

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