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

yannikschaelte · 2020-02-07T22:11:06Z

No description provided.

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

dweindl

Do we really need both the properties and the functions? Can live with it, but seems a bit bloated.

petab/problem.py

dweindl · 2020-02-07T22:12:50Z

petab/problem.py

@@ -347,66 +347,111 @@ def get_noise_distributions(self):
        return measurements.get_noise_distributions(
            measurement_df=self.measurement_df)

+    def _to_mask(v: List, free: bool = True, fixed: bool = True):


What's v?

any vector. maybe arr instead

Not so much about the name, but document arguments.

petab/problem.py

yannikschaelte · 2020-02-07T22:17:08Z

Do we really need both the properties and the functions? Can live with it, but seems a bit bloated.

yeah, don't need the properties, but did not want to destroy backward compatibility in amici+pypesto atm

codecov-io · 2020-02-07T23:31:04Z

Codecov Report

Merging #273 into develop will not change coverage.
The diff coverage is 7.14%.

@@           Coverage Diff            @@
##           develop     #273   +/-   ##
========================================
  Coverage    71.01%   71.01%           
========================================
  Files           22       22           
  Lines         1718     1718           
  Branches       372      372           
========================================
  Hits          1220     1220           
  Misses         418      418           
  Partials        80       80

Impacted Files	Coverage Δ
petab/problem.py	`53.8% <7.14%> (ø)`	⬆️

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* 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 <leonard.schmiester@helmholtz-muenchen.de> * 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 <31767307+yannikschaelte@users.noreply.github.com> * 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 <p.lakrisenko@gmail.com> * 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 <dweindl@users.noreply.github.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * 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 <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> * 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 <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> * 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 <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> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: LeonardSchmiester <leonard.schmiester@helmholtz-muenchen.de> Co-authored-by: Simon Merkt <49190262+MerktSimon@users.noreply.github.com> Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com> Co-authored-by: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>

yannikschaelte and others added 19 commits February 6, 2020 10:40

allow to extract only estimate parameters

279f550

Merge branch 'develop' into fixes_ys

801eee3

add docstrings

3ad1a40

Merge branch 'develop' into fixes_ys

29f717c

return scaled versions of arrays

48b9961

Update petab/problem.py

f62b7ad

Co-Authored-By: Daniel Weindl <dweindl@users.noreply.github.com>

Merge branch 'develop' into fixes_ys

50512ab

Merge branch 'develop' into fixes_ys

e1c7834

add get_observables function

9766c01

add observables test; use observables file in petab test

2f8e2bd

fix typo

a55a86b

move get_observables to ..._ids

fff017d

remove unused arg

79a5d21

add docstring

b2276fd

fix lint

1a41b13

fix pylint

18dfc99

fix flake8

c9f76cb

fix typo

fc636f3

streamline fixed|free|all, and scaled values

202118f

yannikschaelte requested a review from dweindl February 7, 2020 22:11

yannikschaelte self-assigned this Feb 7, 2020

yannikschaelte and others added 2 commits February 7, 2020 23:11

Merge branch 'develop' into fixes_ys

79fe227

fix default args

3af8b13

dweindl approved these changes Feb 7, 2020

View reviewed changes

yannikschaelte added 4 commits February 7, 2020 23:18

fix codacy

7fc5055

address reviewer comment: return empty list

8f0acbb

add docstring#

dfcfa01

add more docstrings

c6dfeb6

yannikschaelte added 3 commits February 8, 2020 16:21

Merge branch 'develop' into fixes_ys

2175297

fix var type error

6560ba0

address reviewer comments

d81b561

yannikschaelte merged commit 538b177 into develop Feb 10, 2020

yannikschaelte deleted the fixes_ys branch February 10, 2020 06:39

yannikschaelte mentioned this pull request Feb 20, 2020

Release 0.1.2 #311

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

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

yannikschaelte commented Feb 7, 2020

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codecov-io commented Feb 7, 2020 •

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

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

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