Develop #284
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Develop #284
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* fix merge error * add petablint yaml test * add parameters test
Closes #103 * Parameter mapping should include all model parameters * Known values should be filled in * Extend and update tests * Refactor parameter mapping * properly handle estimated and non-estimated parameters * Fix wrong parameter scale returned from mapping * ...
* Allow species and compartments in condition table * Updated doc allowing for states etc in condition file * Update pylint: allow lower-case constants * Export __format_version__ * Fix returning floats as strings in case there are parameter names in the condition table Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de>
* Add constants for visualization field IDs * .. and some others * start using them * formatting, ...
Closes #201, closes #241 * Update data format doc for observable table * Add field name constants for observable table * Add observables table to petab.Problem * Update YAML schema and CompositeProblem * Add functions for writing PEtab dataframes to files * Deprecate SBML-observable functions * Implement validation for observable table * Add function for converting SBML-observable models to observable table * Use costants for PEtab table fields * Update PEtab files illustration * Fix most pylint issues (Closes #234) * Update vis to observalble table (Closes #246) No need to check for equal NOISE_DISTRIBUTION and OBSERVABLE_TRANSFORMATION anymore, so they are no longer included in the measurement table, and cannot differ for the same observableId * Fix and update flatten_timepoint_specific_output_overrides Closes #247 Was creating wrong observables before * Address review comments Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Release 0.1.0 Data format: * Introduce observables table instead of SBML assignment rules for defining observation model (#244) (moves observableTransformation and noiseModel from the measurement table to the observables table) * Allow initial concentrations / sizes in condition table (#238) * Fixes and clarifications in the format documentation * Changes in prior columns of the parameter table (#222) * Introduced separate version number of file format, this release being version 1 Library: * Adaptations to new file formats * Various bugfixes and clean-up, especially in visualization and validator * Parameter mapping changed to include all model parameters and not only those differing from the ones defined inside the SBML model * Introduced constants for all field names and string options, replacing most string literals in the code (#228) * Added unit tests and additional format validation steps * Optional parallelization of parameter mapping (#205) * Extended documentation (in-source and example Jupyter notebooks)
* get_optimization_parameter_scales * get_optimization_to_simulation_scale_mapping * add tests
... related to hierarchical optimization, which should be kept outside PEtab
because it is much more useful
... as well as get_default_*_file_name
Release 0.1.1 Library: * Fix parameter mapping: include output parameters not present in SBML model * Fix missing `petab/petab_schema.yaml` in source distribution * Let get_placeholders return an (ordered) list of placeholders * Deprecate `petab.problem.from_folder` and related functions (obsolete after introducing more flexible YAML files for grouping tables and models)
* allow to extract only estimate parameters * add docstrings
* fix #261 * corrected flake8 error - line too long * deleted white space * add F403 to falke8 tests
* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
* Add create_combine_archive for generation of COMBINE archives * Add support for reading PEtab COMBINE archives * Add tests for COMBINE archive r/w
* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments * add parameter properties test * add tests for get/write_parameter_df * add measurements tests * add conditions tests * fix conditions create function * add parameter tests * add observables tests * fixup * add docstrings * address reviewer comments * random edit to see if codacy is happy * random stuff to annoy codecov Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
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