Develop (#284) · PEtab-dev/PEtab@efe91cc

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Develop (#284)
* Add pylint config

* Fixes ys (#237)

* fix merge error

* add petablint yaml test

* add parameters test

* Parameter mapping should include all model parameters (#235)

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 initial concentrations / sizes in condition table (#238)

* 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 <[email protected]>

* Barplots and Replicates with Simulation data (#214)

Fixes #196, fixes #210, fixes #213

* Cleanup visualization (#240)

* Add constants for visualization field IDs
* .. and some others
* start using them
* formatting, ...

* Observables table instead of SBML assignment rules (#244)

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 <[email protected]>

* Release 0.1.0; file format version 1

* Fix parameter mapping: include output parameters not present in SBML model

* Add convenience functions to petab.Problem

* get_optimization_parameter_scales
* get_optimization_to_simulation_scale_mapping
* add tests

* Fix petab/petab_schema.yaml missing in pypi package

* Update pylint ignorelist

* Update README

* Remove obsolete functions

... related to hierarchical optimization, which should be kept outside PEtab

* Let get_placeholders return an (ordered) list of placeholders

because it is much more useful

* Add check for valid identifiers (Closes #179) (#253)

Co-authored-by: Polina Lakrisenko <[email protected]>

* Deprecate petab.problem.from_folder (Closes #245)

... as well as get_default_*_file_name

* Release 0.1.1

* Barplot uniform coloring & yScale=log fix #196 (#255)


* resolves #197

* small fix

* change all barplot colors to blue

* allow to extract only estimate parameters (#256)

* allow to extract only estimate parameters

* add docstrings

* Visu callobs par (#262)

* fix #261

* corrected flake8 error - line too long

* deleted white space

* add F403 to falke8 tests

* Fix handling of numeric observable/noiseFormula in observable table (Fixes #264)

* Add properties for fixed/free and scaled values (#268)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <[email protected]>

Co-authored-by: Daniel Weindl <[email protected]>

* Observables function (#269)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <[email protected]>

* 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 <[email protected]>

* Fix documentation hierarchy

* Add functions to get all of fixed|free, scaled parameter values (#273)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <[email protected]>

* 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 <[email protected]>

* Default column to look for simulation results should be 'simulation'

* PEtab COMBINE archives (#271)

* Add create_combine_archive for generation of COMBINE archives

* Add support for reading PEtab COMBINE archives

* Add tests for COMBINE archive r/w

* Fix sbml_observables_to_table - got broken in eb5453

* Increase test coverage (#278)

* allow to extract only estimate parameters

* add docstrings

* return scaled versions of arrays

* Update petab/problem.py

Co-Authored-By: Daniel Weindl <[email protected]>

* 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 <[email protected]>

Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Yannik Schälte <[email protected]>
Co-authored-by: LeonardSchmiester <[email protected]>
Co-authored-by: Simon Merkt <[email protected]>
Co-authored-by: Polina Lakrisenko <[email protected]>
Co-authored-by: LaraFuhrmann <[email protected]>