Release 0.2.0 #201
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Release 0.2.0 #201
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* plotting at t = inf, draft * move plotting values at t_inf to a separate method * add vertical dashed lines and horisontal lines to inf data points * plot simulations w inf and calculate split axes parameters based on all data to plot * plot with only t = inf * plotting steady-state measurements with replicates * add tests * docstrings Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Fixes ``` SetuptoolsDeprecationWarning: Installing 'petab.visualize.templates' as data is deprecated, please list it in `packages`. ````
Add `Problem.sample_parameter_startpoints_dict` for sampling startpoints as parameter_id=>parameter_value dicts. Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
* minor fixes * add residuals plot * add ax argument * Update petab/visualize/plot_residuals.py Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com> * documentation * rename function * move vis dependances to extras_require * add __all__ --------- Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com>
* add histogram to residuals plot and center zero * text location
* add goodness of fit plot
Handle parametric initial concentrations for cases where the initial concentration parameter does not occur in the model, but only in the parameter table.
* Add PySBModel for handling of PySB models * adds newly introduced model IDs in yaml file to petab.Model, and handles change form `sbml_files` to `model_files` * adds support for the newly introduced model<->petab entity mapping file * Use tentative multilanguage schema * Add mapping table IO * Condition table validation respects mapping table * Add PySB ID parsing and checking Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
Fixes: > DEPRECATION: petab is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at pypa/pip#8559 Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
... and fix some related tox/flake issues
Make sure symbols like `N`, `beta`, ... are used as scalar symbols, and not as sympy functions with the same name. See also ICB-DCM/pyPESTO#1048
Codecov Report
@@ Coverage Diff @@
## main #201 +/- ##
==========================================
- Coverage 78.09% 76.31% -1.79%
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Files 30 34 +4
Lines 2662 3162 +500
Branches 591 765 +174
==========================================
+ Hits 2079 2413 +334
- Misses 425 552 +127
- Partials 158 197 +39
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