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Merge pull request #160 from PEtab-dev/release_0.1.27
Release 0.1.27
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‎.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: [3.7, 3.8, 3.9, "3.10"]
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python-version: ["3.7", "3.10"]
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runs-on: ${{ matrix.platform }}
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steps:
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade pip wheel
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pip install -r .ci_pip_reqs.txt
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pip install .[reports,combine]
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pip install .[reports,combine,tests]
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- name: Run flake8
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run: |

‎CHANGELOG.md

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## 0.1 series
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### 0.1.27
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Features:
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* Added method to check if measurement time is at steady-state by @dilpath in
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https://github.com/PEtab-dev/libpetab-python/pull/124
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* Create dummy simulation conditions dataframe for empty measurements by
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@dilpath in https://github.com/PEtab-dev/libpetab-python/pull/127
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* Validator: Report empty noiseFormula by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/134
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* Speedup visspec assembly / fix deprecation warning by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/135
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* Handle incomplete PEtab problems in `petab.Problem.from_yaml` by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/138
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* Argument forwarding for
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`Problem.get_optimization_to_simulation_parameter_mapping` by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/159
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* Added candidate schema for version 2 by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/142
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* `get_parameter_df`: Allow any collection of parameter tables by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/153,
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@m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/156,
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@dilpath in https://github.com/PEtab-dev/libpetab-python/pull/157
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* Updated visualization example notebooks
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/137,
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/146,
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by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/147
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* Added support for PEtab problems with multiple condition files
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/152
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* Added abstraction for (SBML) models by @dweindl in
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https://github.com/PEtab-dev/libpetab-python/pull/133
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Fixes:
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* Apply get table method before write table method to ensure correct index
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by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/126
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* petablint: Fix incorrect noise-parameter-mismatch error message
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/129
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* Fixed handling of NaN values for parameters in condition table
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/150
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* More informative `petab.calculate` errors
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/151
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Removals:
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* Removed ancient/deprecated default file naming scheme
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/132
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* Removed ancient deprecated functions related to specifying observables/noise
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models inside SBML
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/140
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https://github.com/PEtab-dev/libpetab-python/pull/131
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* Removed deprecated visualization functions
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by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/130
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**New Contributors**
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* @m-philipps made their first contribution in https://github.com/PEtab-dev/libpetab-python/pull/156
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**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.26...v0.1.27
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### 0.1.26
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* Fix SBML Rule handling logic by @dweindl in

‎MANIFEST.in

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include petab/petab_schema.yaml
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recursive-include petab/visualize/templates
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recursive-include petab/schemas *.yaml
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recursive-include petab/visualize/templates *

‎README.md

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[![CI](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml/badge.svg?branch=master)](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml)
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[![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/master/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
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[![CI](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml/badge.svg?branch=main)](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml)
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[![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/main/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
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[![PyPI version](https://badge.fury.io/py/petab.svg)](https://badge.fury.io/py/petab)
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# petab - a Python package for handling PEtab files
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Examples for PEtab Python library usage:
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* [Validation](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_petablint.ipynb)
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* [Visualization](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_visualization.ipynb)
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* [Validation](https://github.com/PEtab-dev/libpetab-python/blob/main/doc/example/example_petablint.ipynb)
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* [Visualization](https://github.com/PEtab-dev/libpetab-python/blob/main/doc/example/example_visualization.ipynb)
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## Getting help

‎doc/conf.py

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import sys
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import warnings
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# Sphinx autosummary does not handle well submodules and functions with
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# identical names if the function is part of __all__ of the parent module.
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# This is way, we get autosummary to create the submodule documentation:
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import petab
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from petab.visualize.plot_data_and_simulation import plot_data_and_simulation
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petab.visualize.plot_data_and_simulation = \
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sys.modules['petab.visualize.plot_data_and_simulation']
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# -- Path setup --------------------------------------------------------------
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'sphinx.ext.autosummary',
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'sphinx.ext.intersphinx',
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'sphinx.ext.viewcode',
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'myst_parser',
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'sphinx_markdown_tables',
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'nbsphinx',
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'myst_nb',
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]
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intersphinx_mapping = {
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autodoc_mock_imports = ['yaml']
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# myst_nb options
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# https://myst-nb.readthedocs.io/en/latest/configuration.html
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nb_execution_mode = "force"
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source_suffix = {
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'.txt': 'restructuredtext',
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'.md': 'markdown',
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}
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# ignore numpy warnings

‎doc/example/example_Isensee/Isensee_visualizationSpecification.tsv

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plot5 JI09_160126_Drg449_444_CycNuc BarPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__ctrl condition 0 Condition pRII_Western 0 pRII_Western Ctrl lin lin
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plot5 JI09_160126_Drg449_444_CycNuc BarPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100 condition 0 Condition pRII_Western 0 pRII_Western IBMX(100)/Fsk(10) lin lin
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plot5 JI09_160126_Drg449_444_CycNuc BarPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10 condition 0 Condition pRII_Western 0 pRII_Western Sp8-Br-cAMPS-AM(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__ctrl time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Ctrl lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Fsk time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Fsk(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Sp8-Br-cAMPS-AM(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc LinePlot MeanAndSD JI09_160201_Drg453-452_CycNuc__ctrl time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Ctrl lin lin
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plot6 JI09_160201_Drg453-452_CycNuc LinePlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Fsk time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Fsk(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc LinePlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Sp8-Br-cAMPS-AM(10) lin lin

‎doc/example/example_Isensee/Isensee_visualizationSpecification_scatterplot.tsv

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plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale
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plot5 JI09_160126_Drg449_444_CycNuc ScatterPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__ctrl condition 0 Condition pRII_Western 0 pRII_Western Ctrl lin lin
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plot5 JI09_160126_Drg449_444_CycNuc ScatterPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100 condition 0 Condition pRII_Western 0 pRII_Western IBMX(100)/Fsk(10) lin lin
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plot5 JI09_160126_Drg449_444_CycNuc ScatterPlot MeanAndSD JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10 condition 0 Condition pRII_Western 0 pRII_Western Sp8-Br-cAMPS-AM(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__ctrl time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Ctrl lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Fsk time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Fsk(10) lin lin
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plot6 JI09_160201_Drg453-452_CycNuc ScatterPlot MeanAndSD JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM time 0 Time [min] Calpha_Microscopy 0 Calpha_Microscopy Sp8-Br-cAMPS-AM(10) lin lin

‎doc/example/example_visualization.ipynb

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‎doc/example/example_visualization_with_visspec.ipynb

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‎doc/example/example_visualization_without_visspec.ipynb

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